264 citations · 2.7k across the 64 of their papers we have counts for
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Iterative Annealing Mechanism Explains the Functions of the GroEL and RNA Chaperones
D. Thirumalai, George H. Lorimer, Changbong Hyeon
Molecular chaperones are ATP-consuming biological machines, which facilitate the folding of proteins and RNA molecules that are kinetically trapped in misfolded states for long tim…
Directly measuring single molecule heterogeneity using force spectroscopy
Michael Hinczewski, Changbong Hyeon, D. Thirumalai
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular…
Extracting folding landscape characteristics of biomolecules using mechanical forces
Changbong Hyeon, Michael Hinczewski, D. Thirumalai
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…
Plasticity of hydrogen bond networks regulates mechanochemistry of cell adhesion complexes
Shaon Chakrabarti, Michael Hinczewski, D. Thirumalai
Mechanical forces acting on cell adhesion receptor proteins regulate a range of cellular functions by formation and rupture of non-covalent interactions with ligands. Typically, fo…
Sequence-dependent folding landscapes of adenine riboswitch aptamers
Jong-Chin Lin, Changbong Hyeon, D. Thirumalai
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 s…
Urea-induced denaturation of PreQ1-riboswitch
Jeseong Yoon, D. Thirumalai, Changbong Hyeon
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…
Entropic stabilization of the folded states of RNA due to macromolecular crowding
Natalia A. Denesyuk, D. Thirumalai
We review the effects of macromolecular crowding on the folding of RNA by considering the simplest scenario when excluded volume interactions between crowding particles and RNA dom…
A Coarse-Grained Model for Predicting RNA Folding Thermodynamics
Natalia A. Denesyuk, D. Thirumalai
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic int…
From mechanical folding trajectories to intrinsic energy landscapes of biopolymers
Michael Hinczewski, J. Christof M. Gebhardt, Matthias Rief +1
In single molecule laser optical tweezer (LOT) pulling experiments a protein or RNA is juxtaposed between DNA handles that are attached to beads in optical traps. The LOT generates…
Helices 2 and 3 are the initiation sites in the PrPc -> PrPsc transition
Jie Chen, Devarajan Thirumalai
It is established that prion protein is the sole causative agent in a number of diseases in humans and animals. However, the nature of conformational changes that the normal cellul…
RNA under Tension: Folding Landscapes, Kinetic Partitioning Mechanism, and Molecular Tensegrity
Jong-Chin Lin, Changbong Hyeon, D. Thirumalai
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…
Determination of factors governing fibrillogenesis of polypeptide chains using lattice models
Mai Suan Li, Nguyen Truong Co, Govardhan Reddy +2
Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The mor…
Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases
U. Deva Priyakumar, Changbong Hyeon, D. Thirumalai +1
Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations u…
Probing the Mechanisms of Fibril Formation Using Lattice Models
Mai Suan Li, D. K. Klimov, J. E. Straub +1
Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While t…
Crowding effects on the mechanical stability and unfolding pathways of Ubiquitin
David L. Pincus, D. Thirumalai
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is…
Minimal models for proteins and RNA: From folding to function
D. L. Pincus, S. S. Cho, C. Hyeon +1
We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group o…
Allosteric communication in Dihydrofolate Reductase: Signaling network and pathways for closed to occluded transition and back
Jie Chen, Ruxandra I. Dima, D. Thirumalai
E. Coli. dihydrofolate reductase (DHFR) undergoes conformational transitions between the closed (CS) and occluded (OS) states which, respectively, describe whether the active site…
Effect of finite size on cooperativity and rates of protein folding
Maksim Kouza, Mai Suan Li, Edward P. O'Brien +2
We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, , using lattice mo…
Dynamics of allosteric transitions in GroEL
Changbong Hyeon, George H. Lorimer, D. Thirumalai
The chaperonin GroEL-GroES, a machine which helps some proteins to fold, cycles through a number of allosteric states, the state, with high affinity for substrate proteins (SPs…
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
Changbong Hyeon, Ruxandra I Dima, D. Thirumalai
Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there a…
Size, shape, and flexibility of RNA structures
Changbong Hyeon, Ruxandra I. Dima, D. Thirumalai
Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and D…
Mechanical unfolding of RNA: From hairpins to structures with internal multiloops
Changbong Hyeon, D. Thirumalai
Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape…
Scenarios for protein aggregation: Molecular Dynamics simulations and Bioinformatic Analysis
Ruxandra I. Dima, Bogdan Tarus, John E. Straub +1
The need to understand the assembly kinetics of fibril formation has become urgent because of the realization that soluble oligomers of amyloidogenic peptides may be even more neur…
Forced-unfolding and force-quench refolding of RNA hairpins
Changbong Hyeon, D. Thirumalai
Using coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of and the loading rate (). The simulations and theoretical analysis have been…