상단메뉴
글로벌메뉴
좌측메뉴
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교수프로필
현창봉
/ School of Computational Sciences
이론 및 계산 생물물리
현대과학에서 생명현상에 대한 탐구노력과 그에 따른 성과들은 실험기술의 발달과 더불어 급격하게 증가하였다. 최근에는 생체분자의 구조변화 및 그에 따르는 생물학적 기능의 동역학을 단일분자 수준에서 직접 관찰하는 것이 가능해지면서, 고전적인 생물학 교과서의 지식을 넘어 물리화학 및 통계역학적 사고에 입각한 좀더 미시적이고도 근본적인 접근법이 생물학 연구에 필요한 시점에 도달하였다. 현창봉 교수의 이론 및 계산 생물물리 연구실에서는 생물계를 복잡계의 하나로 보고, 생체고분자의 동역학 및 상호작용을 분자모형을 이용한 시뮬레이션과 통계역학적인 방법을 통해서 연구하고 있다. 세부연구주제에는 다음과 같은 것들이 있다.
1. 역학적인 힘을 가했을 때 생분자의 반응.
2. RNA와 단백질의 자기조직화 과정.
3. 분자나노모터의 작동원리 이해.
4. 역학적 힘을 이용한 단일분자 실험방법론에 대한 고찰.
5. 다차원에너지공간 특성의 측정과 데이타 해석 방법 제시.
6. 고분자물리.
7. Allostery.
위의 세부적 연구주제들과 더불어 생명현상에 대해 시스템레벨에서의 포괄적인 이해를 갖는 것이 연구실에서 추구하는 궁극적인 목표이다.
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Using Simulations and kinetic network models to reveal the dynamics and functions of riboswitches Title : Using Simulations and kinetic network models to reveal the dynamics and functions of riboswitches Journal : Methods in Enzymology 553, 235-258 (2015)
논문 NUMBER C15015 AUTHOR J.-C. Lin, J. Yoon, C. Hyeon, D. Thirumalai TITLE Using Simulations and kinetic network models to reveal the dynamics and functions of riboswitches ARCHIVE 1410.0652 FILE JOURNAL Methods in Enzymology 553, 235-258 (2015) ABSTRACT
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Effects of macromolecular crowding on the collapse of biopolymers Title : Effects of macromolecular crowding on the collapse of biopolymers Journal : Phys. Rev. Lett. 114, 068303 (2015)
논문 NUMBER C15014 AUTHOR H. Kang, P. A. Pincus, C. Hyeon, D. Thirumalai TITLE Effects of macromolecular crowding on the collapse of biopolymers ARCHIVE FILE JOURNAL Phys. Rev. Lett. 114, 068303 (2015) ABSTRACT
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Communication over the network of binary switches regulates the activation of A2A adenosine receptor Title : Communication over the network of binary switches regulates the activation of A2A adenosine receptor Journal : PLoS Computational Biology 11(2): e1004044 (2015)
논문 NUMBER C15013 AUTHOR Y. Lee, S. Choi, C. Hyeon TITLE Communication over the network of binary switches regulates the activation of A2A adenosine receptor ARCHIVE FILE JOURNAL PLoS Computational Biology 11(2): e1004044 (2015) ABSTRACT
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Programmed folding of DNA origami structures through single-molecule force control Title : Programmed folding of DNA origami structures through single-molecule force control Journal : Nature Communications 5, 5654 (2014)
논문 NUMBER C15012 AUTHOR W. Bae , K. Kim, D. Min, J.-K. Ryu, C. Hyeon, T.-Y. Yoon TITLE Programmed folding of DNA origami structures through single-molecule force control ARCHIVE FILE JOURNAL Nature Communications 5, 5654 (2014) ABSTRACT
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Dynamical Transition and Heterogeneous Hydration Dynamics in RNA Title : Dynamical Transition and Heterogeneous Hydration Dynamics in RNA Journal : J. Phys. Chem. B 118, 7910-7919 (2014)
논문 NUMBER C15011 AUTHOR Yoon, J.-C. Lin, C. Hyeon, D. Thirumalai TITLE Dynamical Transition and Heterogeneous Hydration Dynamics in RNA ARCHIVE FILE JOURNAL J. Phys. Chem. B 118, 7910-7919 (2014) ABSTRACT
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Destabilization of i-motif by submolar concentrations of a monovalent cation Title : Destabilization of i-motif by submolar concentrations of a monovalent cation Journal : J. Phys. Chem. B 118, 4753-4760 (2014)
논문 NUMBER C15010 AUTHOR S. Kim, I.-B. Lee, C. Hyeon, S.-C. Hong TITLE Destabilization of i-motif by submolar concentrations of a monovalent cation ARCHIVE FILE JOURNAL J. Phys. Chem. B 118, 4753-4760 (2014) ABSTRACT
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Evidence of disorder in biological molecules from single molecule pulling experiments Title : Evidence of disorder in biological molecules from single molecule pulling experiments Journal : Phys. Rev. Lett. 112. 138101 (2014)
논문 NUMBER C15009 AUTHOR C. Hyeon, M. Hinczewski, D. Thirumalai TITLE Evidence of disorder in biological molecules from single molecule pulling experiments ARCHIVE FILE JOURNAL Phys. Rev. Lett. 112. 138101 (2014) ABSTRACT
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Development and applications of Coarse Grained models for RNA Title : Development and applications of Coarse Grained models for RNA Journal : Israel J. Chem. 54, 1358 (2014)
논문 NUMBER C15008 AUTHOR C. Hyeon, N. A. Denesyuk, D. Thirumalai TITLE Development and applications of Coarse Grained models for RNA ARCHIVE FILE JOURNAL Israel J. Chem. 54, 1358 (2014) ABSTRACT
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Sequence-dependent folding landscapes of adenine riboswitch aptamers Title : Sequence-dependent folding landscapes of adenine riboswitch aptamers Journal : Phys. Chem. Chem. Phys. 16, 6476 (2014)
논문 NUMBER C15007 AUTHOR J.-C. Lin, C. Hyeon, D. Thirumalai TITLE Sequence-dependent folding landscapes of adenine riboswitch aptamers ARCHIVE FILE JOURNAL Phys. Chem. Chem. Phys. 16, 6476 (2014) ABSTRACT
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Mapping the intramolecular signal transduction of G-protein coupled receptors Title : Mapping the intramolecular signal transduction of G-protein coupled receptors Journal : Proteins: Struct. Func. Bioinfo. 82, 727 (2014)
논문 NUMBER C15006 AUTHOR Y. Lee, S. Choi, C. Hyeon TITLE Mapping the intramolecular signal transduction of G-protein coupled receptors ARCHIVE FILE JOURNAL Proteins: Struct. Func. Bioinfo. 82, 727 (2014) ABSTRACT
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Generalized Iterative Annealing Model for the action of RNA chaperones Title : Generalized Iterative Annealing Model for the action of RNA chaperones Journal : J. Chem. Phys. 139, 121924 (2014)
논문 NUMBER C15005 AUTHOR Changbong Hyeon, D. Thirumalai TITLE Generalized Iterative Annealing Model for the action of RNA chaperones ARCHIVE FILE JOURNAL J. Chem. Phys. 139, 121924 (2014) ABSTRACT
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Urea-induced denaturation of preQ1-riboswitch Title : Urea-induced denaturation of preQ1-riboswitch Journal : J. Am. Chem. Soc. 135, 12112-12121 (2013)
논문 NUMBER C15004 AUTHOR J. Yoon, D. Thirumalai, C. Hyeon TITLE Urea-induced denaturation of preQ1-riboswitch ARCHIVE FILE JOURNAL J. Am. Chem. Soc. 135, 12112-12121 (2013) ABSTRACT
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Real-Time Observation of Multiple Protein-Complex Formation with Single-Molecule FRET Title : Real-Time Observation of Multiple Protein-Complex Formation with Single-Molecule FRET Journal : J. Am. Chem. Soc. 135, 10254 (2013)
논문 NUMBER C15003 AUTHOR W. Bae, M.-G. Choi, C. Hyeon, Y.-K. Shin, T.-Y. Yoon TITLE Real-Time Observation of Multiple Protein-Complex Formation with Single-Molecule FRET ARCHIVE FILE JOURNAL J. Am. Chem. Soc. 135, 10254 (2013) ABSTRACT
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Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism Title : Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism Journal : Nature Communications 4, 1705 (2013)
논문 NUMBER C15002 AUTHOR D. Min, K. Kim, C. Hyeon, Y. H. Cho, Y.-K. Shin, T.-Y. Yoon TITLE Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism ARCHIVE FILE JOURNAL Nature Communications 4, 1705 (2013) ABSTRACT
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Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signaling dynamics Title : Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signaling dynamics Journal : Nature Communications 4, 1505 (2013)
논문 NUMBER C15001 AUTHOR H.-W. Lee, T. Kyung, J. Yoo, T. Kim, C. Chung, J.Y. Ryu, H. Lee, K. Park, S. Lee, W.D. Jones, D.-S. Lim, C. Hyeon, W.D. Heo, T.-Y. Yoon TITLE Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signaling dynamics ARCHIVE FILE JOURNAL Nature Communications 4, 1505 (2013) ABSTRACT
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RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity Title : RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity Journal : J. Phys. Chem. Lett., 3, 3616 (2012)
논문 NUMBER C12017 AUTHOR Jong-Chin Lin, Changbong Hyeon, Dave Thirumalai TITLE RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity ARCHIVE FILE jz301537t.pdf JOURNAL J. Phys. Chem. Lett., 3, 3616 (2012) ABSTRACT Noncoding 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 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 noncoding RNA elements that control gene expression by
undergoing dynamical conformational changes in response to binding of metabolites, lead to
an organization principle in which 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.
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The origin of minus-end directionality and mechanochemistry of Ncd motors Title : The origin of minus-end directionality and mechanochemistry of Ncd motors Journal : PLoS Computational Biology 8, e1002783 (2012)
논문 NUMBER C12016 AUTHOR Biman Jana, Changbong Hyeon. Jose N. Onuchic TITLE The origin of minus-end directionality and mechanochemistry of Ncd motors ARCHIVE FILE JOURNAL PLoS Computational Biology 8, e1002783 (2012) ABSTRACT Adaptation of molecular structure to the ligand chemistry and interaction with the
cytoskeletal filament are key to understanding the mechanochemistry of molecular
motors. Despite the striking structural similarity with kinesin-1, which moves towards
plus-end, Ncd motors exhibit minus-end directionality on microtubules (MTs). Here, by
employing a structure-based model of protein folding, we show that a simple
repositioning of the neck-helix makes the dynamics of Ncd non-processive and minus-
end directed as opposed to kinesin-1. Our computational model shows that Ncd in
solution can have both symmetric and asymmetric conformations with disparate ADP
binding affinity, also revealing that there is a strong correlation between distortion of
motor head and decrease in ADP binding affinity in the asymmetric state. The nucleotide
(NT) free-ADP (w-ADP) state bound to MTs favors the symmetric conformation whose
coiled-coil stalk points to the plus-end. Upon ATP binding, an enhanced flexibility near
the head-neck junction region, which we have identified as the important structural
element for directional motility, leads to reorienting the coiled-coil stalk towards the
minus-end by stabilizing the asymmetric conformation. The minus-end directionality of
the Ncd motor is a remarkable example that demonstrates how motor proteins in the
kinesin superfamily diversify their functions by simply rearranging the structural
elements peripheral to the catalytic motor head domain.
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Hidden complexity in the isomerization dynamics of Holliday junctions Title : Hidden complexity in the isomerization dynamics of Holliday junctions Journal : Nature Chemistry 4, 907 (2012)
논문 NUMBER C12012 AUTHOR Changbong Hyeon, Jinwoo Lee, Jeseong Yoon, Sungchul Hohng, D. Thirumalai TITLE Hidden complexity in the isomerization dynamics of Holliday junctions ARCHIVE FILE nchem.1463.pdf JOURNAL Nature Chemistry 4, 907 (2012) ABSTRACT A plausible consequence of the rugged folding energy landscapes inherent to
biomolecules is that there may be more than one functionally competent folded state.
Indeed, molecule-to-molecule variations in the folding dynamics of enzymes and
ribozymes have recently been identified in single-molecule experiments, but without
systematic quantification or an understanding of their structural origin. Here, using
concepts from glass physics and complementary clustering analysis, we provide a
quantitative method to analyse single-molecule fluorescence resonance energy transfer
(smFRET) data, thereby probing the isomerization dynamics of Holliday junctions,
which display such heterogeneous dynamics over a long observation time (Tobs
≈ 40 s).
We show that the ergodicity of Holliday junction dynamics is effectively broken and that
their conformational space is partitioned into a folding network of kinetically
disconnected clusters. Theory suggests that the persistent heterogeneity of Holliday
junction dynamics is a consequence of internal multiloops with varying sizes and
flexibilities frozen by Mg2+ ions. An annealing experiment using Mg2+ pulses lends
support to this idea by explicitly showing that interconversions between trajectories with
different patterns can be induced.
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Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension Title : Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension Journal : Proc. Natl. Acad. Sci. USA, 109, 14410 (2012)
논문 NUMBER C12009 AUTHOR Won Kyu Kim, Changbong Hyeon, Wokyung Sung TITLE Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA, 109, 14410 (2012) ABSTRACT In addition to thermal noise, which is essential to promote
conformational transitions in
biopolymers, the 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 and
resonant activation. 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.
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Multiple barriers in forced rupture of protein complexes Title : Multiple barriers in forced rupture of protein complexes Journal : J. Chem. Phys. 137, 055103 (2012)
논문 NUMBER C12008 AUTHOR Changbong Hyeon & Dave Thirumalai TITLE Multiple barriers in forced rupture of protein complexes ARCHIVE 1204.1418 FILE JOURNAL J. Chem. Phys. 137, 055103 (2012) ABSTRACT Curvatures in the most probable rupture force (f*) versus log-loading rate (log{r_f})
observed in dy- namic 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*/fc)^{1/ν} ∼ (log
r_f ) with f_c being a critical force in the absence of force, is restricted to 0.5 ≤ ν ≤ 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 if ligand unbinding is assumed to proceed along one-dimensional pulling coordinate, the
dynamics should occur in a energy landscape with multiple-barriers.
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Efficient Functional Delivery of siRNA using Mesoporous Silica Nanoparticles with Ultralarge Pores Title : Efficient Functional Delivery of siRNA using Mesoporous Silica Nanoparticles with Ultralarge Pores Journal : Small 8, 1752 (2012)
논문 NUMBER C12006 AUTHOR Hee-kyung Na, Mi-Hee Kim, Kihyun Park, Soo-Ryoon Ryoo, Kyung Eun Lee, Hyesung Jeon, Ryong Ryoo, Changbong Hyeon, Dal-Hee Min TITLE Efficient Functional Delivery of siRNA using Mesoporous Silica Nanoparticles with Ultralarge Pores ARCHIVE FILE JOURNAL Small 8, 1752 (2012) ABSTRACT Among various nanoparticles, mesoporous silica nanoparticles (MSNs) have attracted
extensive attention for developing efficient drug-delivery systems, mostly due to their
high porosity and biocompatibility. However, due to the small pore size, generally below
5 nm in diameter, potential drugs that are loaded into the pore have been limited to small
molecules. Herein, a small interfering RNA(siRNA) delivery strategy based on MSNs
possessing pores with an average diameter of 23 nm is presented. The siRNA is
regarded as a powerful gene therapeutic agent for treatment of a wide range of disease by
enabling post-transcriptional gene silencing, so-called RNA interference. Highly
efficient, sequence-specific, and technically very simple target gene knockdown is
demonstrated using MSNs with ultralarge pores of size 23 nm in vitro and in vivo
without notable cytotoxicity.
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Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape Title : Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape Journal :
논문 NUMBER C12002 AUTHOR Changbong Hyeon TITLE Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape ARCHIVE 1201.2449 FILE JOURNAL ABSTRACT
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Chain Length Determines the Folding Rates of RNA Title : Chain Length Determines the Folding Rates of RNA Journal : Biophys. J. 102, L11-L13 (2012)
논문 NUMBER C12001 AUTHOR Changbong Hyeon, D. Thirumalai TITLE Chain Length Determines the Folding Rates of RNA ARCHIVE 1201.0795 FILE JOURNAL Biophys. J. 102, L11-L13 (2012) ABSTRACT
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A structural perspective on the dynamics of kinesin motors Title : A structural perspective on the dynamics of kinesin motors Journal : Biophys. J. 101, 2749 (2011)
논문 NUMBER C11024 AUTHOR Changbong Hyeon, Jose N. Onuchic TITLE A structural perspective on the dynamics of kinesin motors ARCHIVE 1111.0174 FILE JOURNAL Biophys. J. 101, 2749 (2011) ABSTRACT Despite significant fluctuation under thermal noise, biological machines in cells perform
their tasks with exquisite precision. Using molecular simulation of a coarse-grained
model and theoretical arguments we envisaged how kinesin, a prototype of biological
machines, generates force and regulates its dynamics to sustain persistent motor action.
A structure based model, which can be versatile in adapting its structure to external
stresses while maintaining its native fold, was employed to account for several features
of kinesin dynamics along the biochemical cycle. This analysis complements our current
understandings of kinesin dynamics and connections to experiments. We propose a
thermodynamic cycle for kinesin that emphasizes the mechanical and regulatory role of
the neck-linker and clarify issues related the motor directionality, and the difference
between the external stalling force and the internal tension responsible for the head-head
coordination. The comparison between the thermodynamic cycle of kinesin and
macroscopic heat engines highlights the importance of structural change as the source of
work production in biomolecular machines.
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Link between allosteric signal transduction and functional dynamics in a multi-subunit enzyme: S-adenosylhomocysteine hydrolase Title : Link between allosteric signal transduction and functional dynamics in a multi-subunit enzyme: S-adenosylhomocysteine hydrolase Journal : J. Am. Chem. Soc. 133, 19807 (2011)
논문 NUMBER C11023 AUTHOR Yoonji Lee, Lak Shin Jeong, Sun Choi, Changbong Hyeon TITLE Link between allosteric signal transduction and functional dynamics in a multi-subunit enzyme: S-adenosylhomocysteine hydrolase ARCHIVE 1110.5980 FILE JOURNAL J. Am. Chem. Soc. 133, 19807 (2011) ABSTRACT S-adenosylhomocysteine hydrolase (SAHH), a cellular enzyme that plays a key role in
methylation reactions including those required for maturation of viral mRNA, is an
important drug target in the discovery of antiviral agents. While targeting the active site is
a straightforward strategy of enzyme inhibition, evidences of allosteric modulation of
active site in many enzymes underscore the molecular origin of signal transduction.
Information of co-evolving sequences in SAHH family and the key residues for
functional dynamics that can be identified using native topology of the enzyme provide
glimpses into how the allosteric signaling network, dispersed over the molecular
structure, coordinates intra- and inter-subunit conformational dynamics. To study the link
between the allosteric communication and functional dynamics of SAHHs, we
performed Brownian dynamics simulations by building a coarse-grained model based on
the holo and ligand-bound structures. The simulations of ligand-induced transition
revealed that the signal of intra-subunit closure dynamics is transmitted to form inter-
subunit contacts, which in turn invoke a precise alignment of active site, followed by the
dimer-dimer rotation that compacts the whole tetrameric structure. Further analyses of
SAHH dynamics associated with ligand binding provided evidence of both induced fit
and population shift mechanisms, and also showed that the transition state ensemble is
akin to the ligand-bound state. Besides the formation of enzyme-ligand contacts at the
active site, the allosteric couplings from the residues distal to the active site is vital to the
enzymatic function.
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Exploring the Energy Landscape of Biopolymers Using Single-Molecule Force Spectroscopy and Molecular Simulations Title : Exploring the Energy Landscape of Biopolymers Using Single-Molecule Force Spectroscopy and Molecular Simulations Journal : Simulations in Nanobiotechnology, Chapter 5
논문 NUMBER C11022 AUTHOR Changbong Hyeon TITLE Exploring the Energy Landscape of Biopolymers Using Single-Molecule Force Spectroscopy and Molecular Simulations ARCHIVE 1009.3697 FILE JOURNAL Simulations in Nanobiotechnology, Chapter 5 ABSTRACT In recent years, single molecule force techniques have opened a new avenue to decipher
the folding landscapes of biopolymers by allowing us to watch and manipulate the
dynamics of individual proteins and nucleic acids. In single molecule force experiments,
quantitative analyses of measurements employing sound theoretical models and
molecular simulations play central role more than any other ?eld. With a brief description
of basic theories for force mechanics and molecular simulation technique using self-
organized polymer (SOP) model, this chapter will discuss various issues in single
molecule force spectroscopy (SMFS) experiments, which include pulling speed
dependent unfolding pathway, measurement of energy landscape roughness, the in uence
of molecular handles in optical tweezers on measurement and molecular motion, and
folding dynamics of biopolymers under force quench condition.
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Capturing the essence of folding and functions of biomolecules using coarse-grained models Title : Capturing the essence of folding and functions of biomolecules using coarse-grained models Journal : Nature Communications 2, 487 (2011)
논문 NUMBER C11021 AUTHOR Changbong Hyeon, D. Thirumalai TITLE Capturing the essence of folding and functions of biomolecules using coarse-grained models ARCHIVE arXiv:1109.5970 FILE JOURNAL Nature Communications 2, 487 (2011) ABSTRACT The distances over which biological molecules and their complexes can function range
from a few nanometres, in the case of folded structures, to millimetres, for example,
during chromosome organization. Describing phenomena that cover such diverse length,
and also time, scales requires models that capture the underlying physics for the
particular length scale of interest. theoretical ideas, in particular, concepts from polymer
physics, have guided the development of coarse-grained models to study folding of
DNA, RNA and proteins. more recently, such models and their variants have been
applied to the functions of biological nanomachines. simulations using coarse-grained
models are now poised to address a wide range of problems in biology.
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Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments Title : Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments Journal : Physical Review Letters 106, 138102 (2011)
논문 NUMBER C11015 AUTHOR Greg Morrison, Changbong Hyeon, Michael Hinczewski, Dave Thirumalai TITLE Compaction and tensile forces determine the accuracy of folding landscape parameters from single molecule pulling experiments ARCHIVE 1103.0425 FILE JOURNAL Physical Review Letters 106, 138102 (2011) ABSTRACT We establish a framework for assessing whether the transition state location of a
biopolymer, which can be inferred from single molecule pulling experiments,
corresponds to the ensemble of structures that have equal probability of reaching either
the folded or unfolded states (Pfold=0.5). Using results for the forced unfolding of a
RNA hairpin, an exactly soluble model, and an analytic theory, we show that Pfold is
solely determined by s, an experimentally measurable molecular tensegrity parameter,
which is a ratio of the tensile force and a compaction force that stabilizes the folded state.
Applications to folding landscapes of DNA hairpins and a leucine zipper with two
barriers provide a structural interpretation of single molecule experimental data. Our
theory can be used to assess whether molecular extension is a good reaction coordinate
using measured free energy profiles.
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Theoretical Perspectives on Protein Folding Title : Theoretical Perspectives on Protein Folding Journal : Annual Review of Biophysics 39, 159 (2010)
논문 NUMBER C10006 AUTHOR Dave Thirumalai, Edward P. OBrien, Greg Morrison, Changbong Hyeon TITLE Theoretical Perspectives on Protein Folding ARCHIVE 1007.3029 FILE JOURNAL Annual Review of Biophysics 39, 159 (2010) ABSTRACT Understanding how monomeric proteins fold under in vitro conditions is crucial to
describing their functions in the cellular context. Significant advances in theory and
experiments have resulted in a conceptual framework for describing the folding mechanisms
of globular proteins.....
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Dynamic Ca2+-Dependent Stimulation of Vesicle Fusion by Membrane-Anchored Synaptotagmin 1 Title : Dynamic Ca2+-Dependent Stimulation of Vesicle Fusion by Membrane-Anchored Synaptotagmin 1 Journal : Science 329, 760 (2010)
논문 NUMBER C10005 AUTHOR Han-Ki Lee, Yoosoo Yang, Zengliu Su, Changbong Hyeon, Tae-Sun Lee, Hong-Won Lee, Dae-Hyuk Kweon, Yeon-Kyun Shin, Tae-Young Yoon TITLE Dynamic Ca2+-Dependent Stimulation of Vesicle Fusion by Membrane-Anchored Synaptotagmin 1 ARCHIVE FILE JOURNAL Science 329, 760 (2010) ABSTRACT In neurons, synaptotagmin 1 (Syt1) is thought to mediate the fusion of synaptic vesicles
with the plasma membrane when presynaptic Ca2+ levels rise. However, in vitro
reconstitution experiments have failed to recapitulate key characteristics of Ca2+-
triggered membrane fusion. Using an in vitro single-vesicle fusion assay, we found that
membrane-anchored Syt1 enhanced Ca2+ sensitivity and fusion speed. This stimulatory
activity of membrane-anchored Syt1 dropped as the Ca2+ level rose beyond
physiological levels. Thus, Syt1 requires the membrane anchor to stimulate vesicle
fusion at physiological Ca2+ levels and may function as a dynamic presynaptic Ca2+
sensor to control the probability of neurotransmitter release.
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Title : Ripping RNA by Force using Gaussian Network Models Journal : J. Phys. Chem. B (2017) vol. 121, 3515-3522
논문 NUMBER AUTHOR C. Hyeon, D. Thirumalai TITLE Ripping RNA by Force using Gaussian Network Models ARCHIVE FILE JOURNAL J. Phys. Chem. B (2017) vol. 121, 3515-3522 ABSTRACT
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Title : A Kinetic Model for the Activation of Mammalian Olfactory Receptor Journal : J. Phys. Chem. B (2017) 121, 1304-1311
논문 NUMBER AUTHOR S. Jang, C. Hyeon TITLE A Kinetic Model for the Activation of Mammalian Olfactory Receptor ARCHIVE FILE JOURNAL J. Phys. Chem. B (2017) 121, 1304-1311 ABSTRACT
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Title : Heterogeneous morphology and dynamics of polyelectrolyte brush condensates in trivalent counterion solution Journal : Macromolecules (2017) 50, 1579-1588
논문 NUMBER AUTHOR L. Liu, P. A. Pincus, C. Hyeon TITLE Heterogeneous morphology and dynamics of polyelectrolyte brush condensates in trivalent counterion solution ARCHIVE FILE JOURNAL Macromolecules (2017) 50, 1579-1588 ABSTRACT
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Title : Quantifying the Heat Disspation from a Molecular Motors Transport Properties in Nonequilibrium Steady State Journal : J. Phys. Chem. B (2017) 121, 1304-1311
논문 NUMBER AUTHOR S. Jang, C. Hyeon TITLE Quantifying the Heat Disspation from a Molecular Motors Transport Properties in Nonequilibrium Steady State ARCHIVE FILE JOURNAL J. Phys. Chem. B (2017) 121, 1304-1311 ABSTRACT
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Title : Decoding Single Molecule Time Traces with Dynamic Disorde Journal : PLoS Comp. Biol. (2016) 12(12), e1005286
논문 NUMBER AUTHOR W. Hwang, I. -B. Lee, S. -C. Hong, C. Hyeon TITLE Decoding Single Molecule Time Traces with Dynamic Disorde ARCHIVE FILE JOURNAL PLoS Comp. Biol. (2016) 12(12), e1005286 ABSTRACT
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Title : Effects of dimethyl sulfoxide on surface water near phospholipid bilayers Journal : Biophys. J. (2016) vol. 111, 2481-2491
논문 NUMBER AUTHOR Y. Lee, P. A. Pincus, C. Hyeon TITLE Effects of dimethyl sulfoxide on surface water near phospholipid bilayers ARCHIVE FILE JOURNAL Biophys. J. (2016) vol. 111, 2481-2491 ABSTRACT
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Title : How are molecular crowding and the spatial organization of a biopolymer interrelated Journal : Soft Matter (2016) vol. 12, 9786-9796
논문 NUMBER AUTHOR C. Jeon, C. Hyeon, Y. Jung, B.-Y. Ha TITLE How are molecular crowding and the spatial organization of a biopolymer interrelated ARCHIVE FILE JOURNAL Soft Matter (2016) vol. 12, 9786-9796 ABSTRACT
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Title : Ultraslow water-mediated transmembrane interactions regulate the activation of A2A adenosine receptor Journal : Biophysical Journal (2016) vol. 111, 1180-1191
논문 NUMBER AUTHOR Y. Lee, S. Kim, S. Choi, C. Hyeon TITLE Ultraslow water-mediated transmembrane interactions regulate the activation of A2A adenosine receptor ARCHIVE FILE JOURNAL Biophysical Journal (2016) vol. 111, 1180-1191 ABSTRACT
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Title : Directly measuring single molecule heterogeneity using force spectroscopy Journal : Proc. Natl. Acad. Sci. USA (2016) vol. 113, E3852-E3861
논문 NUMBER AUTHOR Michael Hinczewski, Changbong Hyeon, D. Thirumalai TITLE Directly measuring single molecule heterogeneity using force spectroscopy ARCHIVE 1605.07294 FILE JOURNAL Proc. Natl. Acad. Sci. USA (2016) vol. 113, E3852-E3861 ABSTRACT
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Title : Contact statistics highlight distinct organizing principles of RNA and proteins Journal : Biophys. J. (2016) vol. 110, 2320-2327
논문 NUMBER AUTHOR Lei Liu, Changbong Hyeon TITLE Contact statistics highlight distinct organizing principles of RNA and proteins ARCHIVE 1604.00472 FILE JOURNAL Biophys. J. (2016) vol. 110, 2320-2327 ABSTRACT
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Title : Confinement-induced glassy dynamics in a model for chromosome organization Journal : Phys. Rev. Lett. (2015) vol. 115, 198102
논문 NUMBER AUTHOR H. Kang, Y.-G. Yoon, D. Thirumalai, C. Hyeon TITLE Confinement-induced glassy dynamics in a model for chromosome organization ARCHIVE 1506.01089 FILE JOURNAL Phys. Rev. Lett. (2015) vol. 115, 198102 ABSTRACT
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Title : Unexpected swelling of stiff DNA in a polydisperse crowded environment Journal : J. Am. Chem. Soc. (2015) vol. 137, 10970-10978
논문 NUMBER AUTHOR H. Kang, N. M. Toan, C. Hyeon, D. Thirumalai TITLE Unexpected swelling of stiff DNA in a polydisperse crowded environment ARCHIVE 1505.01623 FILE JOURNAL J. Am. Chem. Soc. (2015) vol. 137, 10970-10978 ABSTRACT
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Title : Deciphering kinetic information from single molecule FRET data that show slow transitions Journal : J. Phys. Chem. B. (2015) vol. 119, 6974–6978
논문 NUMBER AUTHOR S. E. Kim, I. -B. Lee, C. Hyeon, S.-C. Hong TITLE Deciphering kinetic information from single molecule FRET data that show slow transitions ARCHIVE FILE JOURNAL J. Phys. Chem. B. (2015) vol. 119, 6974–6978 ABSTRACT Single-molecule FRET is one of the most
powerful and widely used biophysical techniques in biological
sciences. It, however, often suffers from limitations such as
weak signal and limited measurement time intrinsic to single-
molecule fluorescence measurements. Despite several amelio-
rative measures taken to increase measurement time, it is
nearly impossible to acquire meaningful kinetic information on
a molecule if conformational transitions of the molecule are
ultraslow such that transition times (⟨τ⟩orig) are comparable to
or longer than measurement times (δt) limited by the finite
lifetime of fluorescent dye. Here, to extract a reliable and
accurate mean transition time from a series of short time traces
with ultraslow kinetics, we suggest a scheme called sHaRPer (serialized Handshaking Repeated Permutation with end removal) that concatenates multiple time traces. Because data acquisition frequency f and measurement time (δt) affect the estimation of mean transition time (⟨τ⟩), we provide mathematical criteria that f, δt, and ⟨τ⟩ should satisfy to make ⟨τ⟩ close enough to ⟨τ⟩orig. Although application of the sHaRPer method has a potential risk of distorting the time constants of individual kinetic phases if the data are described with kinetic partitioning, we also provide criteria to avoid such distortion. Our sHaRPer method is a useful way to handle single-molecule data with slow transition kinetics. This study provides a practical guide to use sHaRPer.
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Title : Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover Journal : Science (2015) vol. 347, 1485
논문 NUMBER AUTHOR J.-K. Ryu, D. Min, S.-H. Rah, S. J. Kim, Y. Park, H. Kim, C. Hyeon, H. M. Kim, R. Jahn, T.-Y. Yoon TITLE Spring-loaded unraveling of a single SNARE complex by NSF in one round of ATP turnover ARCHIVE FILE JOURNAL Science (2015) vol. 347, 1485 ABSTRACT
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Title : Using Simulations and kinetic network models to reveal the dynamics and functions of riboswitches Journal : Methods in Enzymology (2015) vol. 553, 235-258
논문 NUMBER AUTHOR J.-C. Lin, J. Yoon, C. Hyeon, D. Thirumalai TITLE Using Simulations and kinetic network models to reveal the dynamics and functions of riboswitches ARCHIVE FILE JOURNAL Methods in Enzymology (2015) vol. 553, 235-258 ABSTRACT
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Title : Effects of macromolecular crowding on the collapse of biopolymers Journal : Phys. Rev. Lett. (2015) vol. 114, 068303
논문 NUMBER AUTHOR H. Kang, P. A. Pincus, C. Hyeon, D. Thirumalai TITLE Effects of macromolecular crowding on the collapse of biopolymers ARCHIVE 1409.5663 FILE JOURNAL Phys. Rev. Lett. (2015) vol. 114, 068303 ABSTRACT
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Title : Communication over the network of binary switches regulates the activation of A2A adenosine receptor Journal : PLoS Comp. Biol. (2015) 11(2): e1004044.
논문 NUMBER AUTHOR Y. Lee, S. Choi, C. Hyeon TITLE Communication over the network of binary switches regulates the activation of A2A adenosine receptor ARCHIVE 1411.5360 FILE JOURNAL PLoS Comp. Biol. (2015) 11(2): e1004044. ABSTRACT
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Title : Programmed folding of DNA origami structures through single-molecule force control Journal : Nat. Commun (2014) vol. 5, 5654
논문 NUMBER AUTHOR W. Bae , K. Kim, D. Min, J.-K. Ryu, C. Hyeon, T.-Y. Yoon TITLE Programmed folding of DNA origami structures through single-molecule force control ARCHIVE FILE JOURNAL Nat. Commun (2014) vol. 5, 5654 ABSTRACT
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Title : Destabilization of i-motif by submolar concentrations of a monovalent cation Journal : J. Phys. Chem. B. (2014) vol. 118, 4753-4760.
논문 NUMBER AUTHOR S. Kim, I.-B. Lee, C. Hyeon, S.-C. Hong TITLE Destabilization of i-motif by submolar concentrations of a monovalent cation ARCHIVE FILE JOURNAL J. Phys. Chem. B. (2014) vol. 118, 4753-4760. ABSTRACT
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Title : Evidence of disorder in biological molecules from single molecule pulling experiments Journal : Phys. Rev. Lett.(2014) 112, 138101
논문 NUMBER AUTHOR C. Hyeon, M. Hinczewski, D. Thirumalai TITLE Evidence of disorder in biological molecules from single molecule pulling experiments ARCHIVE 1402.6683 FILE JOURNAL Phys. Rev. Lett.(2014) 112, 138101 ABSTRACT
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Title : Development and applications of Coarse Grained models for RNA Journal : Israel J. Chem. (2014) vol. 54, 1358-1373
논문 NUMBER AUTHOR C. Hyeon, N. A. Denesyuk, D. Thirumalai TITLE Development and applications of Coarse Grained models for RNA ARCHIVE 1402.6030 FILE JOURNAL Israel J. Chem. (2014) vol. 54, 1358-1373 ABSTRACT
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Title : Dynamical Transition and Heterogeneous Hydration Dynamics in RNA Journal : J. Phys. Chem. B. (2014) vol. 118, 7910-7919
논문 NUMBER AUTHOR J. Yoon, J.-C. Lin, C. Hyeon, D. Thirumalai TITLE Dynamical Transition and Heterogeneous Hydration Dynamics in RNA ARCHIVE FILE JOURNAL J. Phys. Chem. B. (2014) vol. 118, 7910-7919 ABSTRACT
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Title : Destabilization of i-motif by submolar concentrations of a monovalent cation Journal : J. Phys. Chem. B. (2014) vol. 118, 4753-4760.
논문 NUMBER AUTHOR S. Kim, I.-B. Lee, C. Hyeon, S.-C. Hong TITLE Destabilization of i-motif by submolar concentrations of a monovalent cation ARCHIVE FILE JOURNAL J. Phys. Chem. B. (2014) vol. 118, 4753-4760. ABSTRACT
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Title : Evidence of disorder in biological molecules from single molecule pulling experiments Journal : Phys. Rev. Lett. (2014) vol. 112, 138101
논문 NUMBER AUTHOR C. Hyeon, M. Hinczewski, D. Thirumalai TITLE Evidence of disorder in biological molecules from single molecule pulling experiments ARCHIVE FILE JOURNAL Phys. Rev. Lett. (2014) vol. 112, 138101 ABSTRACT
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Title : Sequence-dependent folding landscapes of adenine riboswitch aptamers Journal : Phys. Chem. Chem. Phys. (2014) vol. 16, 6376
논문 NUMBER AUTHOR J.-C. Lin, C. Hyeon, D. Thirumalai TITLE Sequence-dependent folding landscapes of adenine riboswitch aptamers ARCHIVE FILE JOURNAL Phys. Chem. Chem. Phys. (2014) vol. 16, 6376 ABSTRACT
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Title : Mapping the intramolecular signal transduction of G-protein coupled receptors Journal : Proteins: Struct. Func. Bioinfo. (2014) vol. 82, 727-743
논문 NUMBER AUTHOR Y. Lee, S. Choi, & C. Hyeon TITLE Mapping the intramolecular signal transduction of G-protein coupled receptors ARCHIVE FILE JOURNAL Proteins: Struct. Func. Bioinfo. (2014) vol. 82, 727-743 ABSTRACT
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Title : Generalized Iterative Annealing Model for the action of RNA chaperones Journal : J. Chem. Phys. (2013) vol. 139, 121924
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai TITLE Generalized Iterative Annealing Model for the action of RNA chaperones ARCHIVE FILE JOURNAL J. Chem. Phys. (2013) vol. 139, 121924 ABSTRACT
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Title : Urea-induced denaturation of preQ1-riboswitch Journal : J. Am. Chem. Soc. (2013) vol. 135, 12112
논문 NUMBER AUTHOR J. Yoon, D. Thirumalai, C. Hyeon TITLE Urea-induced denaturation of preQ1-riboswitch ARCHIVE FILE JOURNAL J. Am. Chem. Soc. (2013) vol. 135, 12112 ABSTRACT
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Title : Real-Time Observation of Multiple Protein-Complex Formation with Single-Molecule FRET Journal : J. Am. Chem. Soc. (2013) vol. 135, 10254
논문 NUMBER AUTHOR W. Bae, M.-G. Choi, C. Hyeon, Y.-K. Shin, T.-Y. Yoon TITLE Real-Time Observation of Multiple Protein-Complex Formation with Single-Molecule FRET ARCHIVE FILE JOURNAL J. Am. Chem. Soc. (2013) vol. 135, 10254 ABSTRACT
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Title : Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism Journal : Nat. Commun. (2013) vol. 4, 1705
논문 NUMBER AUTHOR D. Min, K. Kim, C. Hyeon, Y. H. Cho, Y.-K. Shin, T.-Y. Yoon TITLE Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism ARCHIVE FILE JOURNAL Nat. Commun. (2013) vol. 4, 1705 ABSTRACT
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Title : Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signaling dynamics Journal : Nat. Commun. (2013) vol. 4, 1505
논문 NUMBER AUTHOR H.-W. Lee, T. Kyung, J. Yoo, T. Kim, C. Chung, J.Y. Ryu, H. Lee, K. Park, S. Lee, W.D. Jones, D.-S. Lim, C. Hyeon, W.D. Heo, T.-Y. Yoon TITLE Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signaling dynamics ARCHIVE FILE JOURNAL Nat. Commun. (2013) vol. 4, 1505 ABSTRACT
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Title : RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity Journal : J. Phys. Chem. Lett. (2012) vol. 3, 3616
논문 NUMBER AUTHOR J.-C. Lin, C. Hyeon, D. Thirumalai TITLE RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity ARCHIVE FILE JOURNAL J. Phys. Chem. Lett. (2012) vol. 3, 3616 ABSTRACT
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Title : The origin of minus-end directionality and mechanochemistry of Ncd motors Journal : PLoS Comp. Biol. (2012) vol. 8, e1002783
논문 NUMBER AUTHOR B. Jana, C. Hyeon, J. N. Onuchic TITLE The origin of minus-end directionality and mechanochemistry of Ncd motors ARCHIVE FILE JOURNAL PLoS Comp. Biol. (2012) vol. 8, e1002783 ABSTRACT
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Title : Hidden Complexity in the Isomerization Dynamics of Holliday Junctions Journal : Nature Chem. (2012) vol.4, 907
논문 NUMBER AUTHOR C. Hyeon, J. Lee, J. Yoon, S. Hohng, D. Thirumalai TITLE Hidden Complexity in the Isomerization Dynamics of Holliday Junctions ARCHIVE FILE JOURNAL Nature Chem. (2012) vol.4, 907 ABSTRACT
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Title : Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension Journal : Proc. Natl. Acad. Sci. (2012) vol. 109, 14410
논문 NUMBER AUTHOR W. K. Kim, C. Hyeon, W. Sung TITLE Weak temporal signals can synchronize and accelerate the transition dynamics of biopolymers under tension ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. (2012) vol. 109, 14410 ABSTRACT
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Title : Multiple barriers in forced rupture of protein complexes Journal : J. Chem. Phys. (2012) vol. 137, 055103
논문 NUMBER AUTHOR C. Hyeon and. D. Thirumalai TITLE Multiple barriers in forced rupture of protein complexes ARCHIVE FILE JOURNAL J. Chem. Phys. (2012) vol. 137, 055103 ABSTRACT
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Title : Efficient Functional Delivery of siRNA using Mesoporous Silica Nanoparticles with Ultralarge Pores Journal : Small (2012) vol. 8, 1752
논문 NUMBER AUTHOR H.-K. Na, M.-H. Kim, K. Park, S.-R. Ryoo, K.E. Lee, H. Jeon, R. Ryoo, C. Hyeon, D.-H. Min TITLE Efficient Functional Delivery of siRNA using Mesoporous Silica Nanoparticles with Ultralarge Pores ARCHIVE FILE JOURNAL Small (2012) vol. 8, 1752 ABSTRACT
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Title : Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape Journal : Bull. Korean Chem. Soc. (2012) vol. 33, 897
논문 NUMBER AUTHOR C. Hyeon TITLE Force-induced Unbinding Dynamics in a Multidimensional Free Energy Landscape ARCHIVE FILE JOURNAL Bull. Korean Chem. Soc. (2012) vol. 33, 897 ABSTRACT
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Title : Chain Length Determines the Folding Rates of RNA Journal : Biophys. J. (2012) 102, L11-L13
논문 NUMBER AUTHOR C. Hyeon, D. Thirumalai TITLE Chain Length Determines the Folding Rates of RNA ARCHIVE FILE JOURNAL Biophys. J. (2012) 102, L11-L13 ABSTRACT
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Title : A structural perspective on the dynamics of kinesin motors Journal : Biophys. J. (2011) vol. 101, 2749
논문 NUMBER AUTHOR C.Hyeon, J. N. Onuchic TITLE A structural perspective on the dynamics of kinesin motors ARCHIVE FILE JOURNAL Biophys. J. (2011) vol. 101, 2749 ABSTRACT
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Title : Link between Allosteric Signal Transduction and Functional Dynamics in a Multisubunit Enzyme: S-Adenosylhomocysteine Hydrolase Journal : J. Am. Chem. Soc. (2011) 113, 19807-19815
논문 NUMBER AUTHOR Y. Lee, LS Jeong, S. Choi, C. Hyeon TITLE Link between Allosteric Signal Transduction and Functional Dynamics in a Multisubunit Enzyme: S-Adenosylhomocysteine Hydrolase ARCHIVE FILE JOURNAL J. Am. Chem. Soc. (2011) 113, 19807-19815 ABSTRACT
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Title : Capturing the essence of folding and functions of biomolecules using Coarse-Grained models Journal : Nature Communication (2011) vol. 2, 487
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai TITLE Capturing the essence of folding and functions of biomolecules using Coarse-Grained models ARCHIVE FILE JOURNAL Nature Communication (2011) vol. 2, 487 ABSTRACT
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Title : Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments Journal : Phys. Rev. Lett. (2011) 106, 138102
논문 NUMBER AUTHOR Greg Morrison, Changbong Hyeon, Michael Hinczewski TITLE Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments ARCHIVE FILE prl2011.pdf JOURNAL Phys. Rev. Lett. (2011) 106, 138102 ABSTRACT We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching either the folded or unfolded states (Pfold=0.5). Using results for the forced unfolding of a RNA hairpin, an exactly soluble model, and an analytic theory, we show that Pfold is solely determined by s, an experimentally measurable molecular tensegrity parameter, which is a ratio of the tensile force and a compaction force that stabilizes the folded state. Applications to folding landscapes of DNA hairpins and a leucine zipper with two barriers provide a structural interpretation of single molecule experimental data. Our theory can be used to assess whether molecular extension is a good reaction coordinate using measured free energy profiles.
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Title : Theoretical Perspectives on Protein Folding Journal : Annu. Rev. Biophys. (2010) vol. 39, 159-183
논문 NUMBER AUTHOR D. Thirumalai, EP Obrien, G. Morrison, C. Hyeon TITLE Theoretical Perspectives on Protein Folding ARCHIVE FILE JOURNAL Annu. Rev. Biophys. (2010) vol. 39, 159-183 ABSTRACT
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Title : Dynamic Ca2+-dependent stimulation of vesicle fusion by membrane-anchored synaptotagmin 1 Journal : Science (2010) vol. 328, 760-763
논문 NUMBER AUTHOR H. -K. Lee, Y. Yang, Z. Su, C. Hyeon, T. -S. Lee, H. -W. Lee, D. -H. Kwon, Y. -K. Shin and T. -Y. Yoon TITLE Dynamic Ca2+-dependent stimulation of vesicle fusion by membrane-anchored synaptotagmin 1 ARCHIVE FILE JOURNAL Science (2010) vol. 328, 760-763 ABSTRACT
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Title : Urea destabilizes RNA by forming stacking interaction and multiple hydrogen bonds with nucleic acid bases Journal : J. Am. Chem. Soc. (2009) Vol. 131, 17759-17761
논문 NUMBER AUTHOR U. D. Priyakumar, C. Hyeon, D. Thirumalai and A. D. MacKerell Jr. TITLE Urea destabilizes RNA by forming stacking interaction and multiple hydrogen bonds with nucleic acid bases ARCHIVE FILE JOURNAL J. Am. Chem. Soc. (2009) Vol. 131, 17759-17761 ABSTRACT
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Title : Refolding dynamics of stretched biopolymers upon force-quench Journal : Proc. Natl. Acad. Sci. USA (2009) Vol. 106, 20288-20293
논문 NUMBER AUTHOR C. Hyeon, G. Morrison, D. L. Pincus and D. Thirumalai TITLE Refolding dynamics of stretched biopolymers upon force-quench ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2009) Vol. 106, 20288-20293 ABSTRACT
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Title : Metal Ion Dependence of Cooperative Collapse Transitions in RNA Journal : J. Mol. Biol. (2009) Vol. 393, 753-764
논문 NUMBER AUTHOR S. Moghaddam, G. Caliskan, S. Chauhan, C. Hyeon, R. M. Briber, D. Thirumalai and S. A. Woodson TITLE Metal Ion Dependence of Cooperative Collapse Transitions in RNA ARCHIVE FILE JOURNAL J. Mol. Biol. (2009) Vol. 393, 753-764 ABSTRACT
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Title : Kinesins Backsteps under Mechanical Load Journal : Phys. Chem. Chem. Phys. (2009) vol. 11, 4899-4910
논문 NUMBER AUTHOR C. Hyeon, S. Klumpp and J. N. Onuchic TITLE Kinesins Backsteps under Mechanical Load ARCHIVE FILE JOURNAL Phys. Chem. Chem. Phys. (2009) vol. 11, 4899-4910 ABSTRACT
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Title : Ligand-induced global transition in the catalytic domain of protein kinase A Journal : Proc. Natl. Acad. Sci. USA (2009) vol. 106, 3023-3028
논문 NUMBER AUTHOR C. Hyeon, P. A. Jennings, J. A. Adams and J. N. Onuchic TITLE Ligand-induced global transition in the catalytic domain of protein kinase A ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2009) vol. 106, 3023-3028 ABSTRACT
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Title : Force dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes Journal : Proc. Natl. Acad. Sci. USA (2008) vol. 105, 9604-9609
논문 NUMBER AUTHOR C. Hyeon, G. Morrison and D. Thirumalai TITLE Force dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2008) vol. 105, 9604-9609 ABSTRACT
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Title : Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the stability of RNA hairpins Journal : J. Am. Chem. Soc. (2008) vol. 130. 7364-7372
논문 NUMBER AUTHOR D. L. Pincus, C. Hyeon and D. Thirumalai TITLE Effects of Trimethylamine N-Oxide (TMAO) and Crowding Agents on the stability of RNA hairpins ARCHIVE FILE JOURNAL J. Am. Chem. Soc. (2008) vol. 130. 7364-7372 ABSTRACT
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Title : Kinetics of loop formation in polymer chains Journal : J. Phys. Chem. B (2008) vol. 112 6094-6106
논문 NUMBER AUTHOR N. M. Toan, G. Morrison, C. Hyeon and D. Thirumalai TITLE Kinetics of loop formation in polymer chains ARCHIVE FILE JOURNAL J. Phys. Chem. B (2008) vol. 112 6094-6106 ABSTRACT
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Title : Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins Journal : J. Am. Chem. Soc. (2008) vol. 130 1538-1539
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai TITLE Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins ARCHIVE FILE JOURNAL J. Am. Chem. Soc. (2008) vol. 130 1538-1539 ABSTRACT
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Title : Revealing the bifurcation in the unfolding pathways of GFP using single molecule experiments and simulations Journal : Proc. Natl. Acad. Sci. USA (2007) vol. 104 20268-20273
논문 NUMBER AUTHOR M. Michkler, R. I. Dima, H. Dietz, C. Hyeon, D. Thirumalai and M. Rief TITLE Revealing the bifurcation in the unfolding pathways of GFP using single molecule experiments and simulations ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2007) vol. 104 20268-20273 ABSTRACT
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Title : Mechanical control of the directional stepping dynamics of the kinesin motor Journal : Proc. Natl. Acad. Sci. (2007) vol. 104 17382-17387
논문 NUMBER AUTHOR C. Hyeon and J. N. Onuchic, TITLE Mechanical control of the directional stepping dynamics of the kinesin motor ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. (2007) vol. 104 17382-17387 ABSTRACT
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Title : Stretching Homopolymers Journal : Macromolecules (2007) vol. 40 7343-7353
논문 NUMBER AUTHOR G. Morrison, C. Hyeon, N. M. Toan, B. -Y. Ha and D. Thirumalai TITLE Stretching Homopolymers ARCHIVE FILE JOURNAL Macromolecules (2007) vol. 40 7343-7353 ABSTRACT
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Title : Charge density of divalent metal cations determines RNA stability Journal : Soc. (2007) vol. 129 2676-2682
논문 NUMBER AUTHOR E. Koculi, C. Hyeon, D. Thirumalai, and S. A. Woodson, J. Am. Chem TITLE Charge density of divalent metal cations determines RNA stability ARCHIVE FILE JOURNAL Soc. (2007) vol. 129 2676-2682 ABSTRACT
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Title : Internal strain regulates the nucleotide binding site of the kinesin leading head Journal : Proc. Natl. Acad. Sci. USA (2007) vol. 104 2175-2180
논문 NUMBER AUTHOR C. Hyeon and J. N. Onuchic TITLE Internal strain regulates the nucleotide binding site of the kinesin leading head ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2007) vol. 104 2175-2180 ABSTRACT
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Title : Mechanical unfolding of RNA: From hairpins to structures with internal multiloops Journal : Biophys. J. (2007) vol. 92 731-743
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai TITLE Mechanical unfolding of RNA: From hairpins to structures with internal multiloops ARCHIVE FILE JOURNAL Biophys. J. (2007) vol. 92 731-743 ABSTRACT
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Title : Dynamics of allosteric transitions in GroEL Journal : Proc. Natl. Acad. Sci. USA (2006) vol. 103 18939-18944
논문 NUMBER AUTHOR C. Hyeon, G.H. Lorimer and D. Thirumalai TITLE Dynamics of allosteric transitions in GroEL ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2006) vol. 103 18939-18944 ABSTRACT
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Title : Size, Shape, and flexibility of RNA structures Journal : Phys. (2006) vol. 125 194905
논문 NUMBER AUTHOR C. Hyeon, R. I. Dima, and D. Thirumalai, J. Chem TITLE Size, Shape, and flexibility of RNA structures ARCHIVE FILE JOURNAL Phys. (2006) vol. 125 194905 ABSTRACT
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Title : Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins Journal : Structure (2006) vol. 14 1633-1645
논문 NUMBER AUTHOR C. Hyeon, R.I. Dima, and D. Thirumalai TITLE Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins ARCHIVE FILE JOURNAL Structure (2006) vol. 14 1633-1645 ABSTRACT
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Title : Forced-Unfolding and Force-Quench Refolding of RNA Hairpins Journal : Biophys. J. (2006) vol. 90 3410-3427
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai TITLE Forced-Unfolding and Force-Quench Refolding of RNA Hairpins ARCHIVE FILE JOURNAL Biophys. J. (2006) vol. 90 3410-3427 ABSTRACT
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Title : Kinetics of interior loop formation in semiflexible chains Journal : J. Chem. Phys. (2006) vol. 124 104905
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai, TITLE Kinetics of interior loop formation in semiflexible chains ARCHIVE FILE JOURNAL J. Chem. Phys. (2006) vol. 124 104905 ABSTRACT
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Title : Persistence Length Changes Dramatically as RNA Folds Journal : Phys. Rev. Lett. (2005) vol. 95 268303
논문 NUMBER AUTHOR G. Caliskan, C. Hyeon, U. Perez-Salas, B.M. Briber, S.A. Woodson, and D. Thirumalai TITLE Persistence Length Changes Dramatically as RNA Folds ARCHIVE FILE JOURNAL Phys. Rev. Lett. (2005) vol. 95 268303 ABSTRACT
-
Title : Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures Journal : J. Mol. Biol. (2005) vol. 347 53-69
논문 NUMBER AUTHOR R.I. Dima, C. Hyeon, and D. Thirumalai TITLE Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures ARCHIVE FILE JOURNAL J. Mol. Biol. (2005) vol. 347 53-69 ABSTRACT
-
Title : Mechanical unfolding of RNA hairpins Journal : Proc. Natl. Acad. Sci. USA (2005) vol. 102 6789-6794
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai TITLE Mechanical unfolding of RNA hairpins ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2005) vol. 102 6789-6794 ABSTRACT
-
Title : Can energy landscape roughness of proteins and RNA be measured using mechanical unfolding experiments? Journal : Proc. Natl. Acad. Sci. USA (2003) vol. 100 10249-10253
논문 NUMBER AUTHOR C. Hyeon and D. Thirumalai TITLE Can energy landscape roughness of proteins and RNA be measured using mechanical unfolding experiments? ARCHIVE FILE JOURNAL Proc. Natl. Acad. Sci. USA (2003) vol. 100 10249-10253 ABSTRACT
-
Title : One-pot Template Synthesis and Properties of a Molecular Bowl: Dodecaaza Macrotetracycle with mu(3)-Oxo and mu(3)-Hydroxo Tricopper(II) Cores Journal : J. Am. Chem. Soc. (1998) vol. 120, 3819-3820
논문 NUMBER AUTHOR M. Paik Suh, M.Y. Han, J.H.Lee K.S.Min, and C. Hyeon. TITLE One-pot Template Synthesis and Properties of a Molecular Bowl: Dodecaaza Macrotetracycle with mu(3)-Oxo and mu(3)-Hydroxo Tricopper(II) Cores ARCHIVE FILE JOURNAL J. Am. Chem. Soc. (1998) vol. 120, 3819-3820 ABSTRACT
-
Title : Effects of a quantum-mechanically driven two-state gating mode on the diffusion-influenced bimolecular reactions Journal : Phys. (1997) vol. 107 9864
논문 NUMBER AUTHOR Y. Jung, C. Hyeon, S. Shin, and S. Lee, J. Chem TITLE Effects of a quantum-mechanically driven two-state gating mode on the diffusion-influenced bimolecular reactions ARCHIVE FILE JOURNAL Phys. (1997) vol. 107 9864 ABSTRACT
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- 2010-현재 고등과학원 계산과학부 교수
- 2008-2009 중앙대학교 화학과 조교수
- 2006-2008 UC San Diego, 물리학과 박사후 연구원
- 2000-2005 화학물리 박사, 메릴랜드 대학교
- 1995-1997, 화학 석사, 서울대학교
- 1991-1995, 화학 학사, 서울대학교
- Office:7302 / TEL) 82-2-958-3810 / FAX) 82-2-958-3820
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