Search Results - "Klimov, DK"

Early events in RNA folding by Thirumalai, D, Lee, N, Woodson, S A, Klimov, D

“…We describe a conceptual framework for understanding the way large RNA molecules fold based on the notion that their free-energy landscape is rugged. A key…”
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Emerging ideas on the molecular basis of protein and peptide aggregation by Thirumalai, D, Klimov, DK, Dima, RI

“…Several neurodegenerative diseases are associated with the unfolding and subsequent fibrillization of proteins. Although neither the assembly mechanism nor the…”
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Mechanisms and Kinetics of β -Hairpin Formation by Klimov, D K, Thirumalai, D

“…Thermodynamics and kinetics of off-lattice models with side chains for the β -hairpin fragment of immunoglobulin-binding protein and its variants are reported…”
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Simulations of β-Hairpin Folding Confined to Spherical Pores Using Distributed Computing by Klimov, D. K., Newfield, D., Thirumalai, D.

“…We report the thermodynamics and kinetics of an off-lattice Go model β-hairpin from Ig-binding protein confined to an inert spherical pore. Confinement…”
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Native Topology Determines Force-Induced Unfolding Pathways in Globular Proteins by Klimov, D. K., Thirumalai, D.

“…Single-molecule manipulation techniques reveal that stretching unravels individually folded domains in the muscle protein titin and the extracellular matrix…”
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Viscosity Dependence of the Folding Rates of Proteins by Klimov, D. K., Thirumalai, D.

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Symmetric Connectivity of Secondary Structure Elements Enhances the Diversity of Folding Pathways by Klimov, Dmitri K., Thirumalai, D.

“…The influence of native connectivity of secondary structure elements (SSE) on folding is studied using coarse-grained models of proteins with mixed α and β…”
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Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models by Thirumalai, D, Klimov, D.K.

“…Considerable insights into the mechanisms and timescales of protein folding have been obtained from detailed studies of minimal off-lattice models. These…”
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Thermal denaturation and folding rates of single domain proteins: size matters by Li, Mai Suan, Klimov, D.K, Thirumalai, D

“…We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go…”
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Criterion that determines the foldability of proteins by Klimov, DK, Thirumalai, D

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Multiple protein folding nuclei and the transition state ensemble in two-state proteins by Klimov, D.K., Thirumalai, D.

“…Using exhaustive simulations of lattice models with side‐chains, we show that optimized two‐state folders reach the native state by a nucleation‐collapse…”
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Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains by Klimov, D K, Thirumalai, D

“…Protein engineering experiments and Phi(F)-value analysis of SH3 domains reveal that their transition state ensemble (TSE) is conformationally restricted, i.e…”
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Caging Helps Proteins Fold by Thirumalai, D., Klimov, Dmitri K., Lorimer, George H.

“…The quest to answer the question of how proteins fold spontaneously has lead to significant developments on theoretical, experimental, and computational fronts…”
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Finite size effects on thermal denaturation of globular proteins by MAI SUAN LI, KLIMOV, Dmitri K, THIRUMALAI, D

“…Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omegac, scales as Nzeta,…”
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Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism by Klimov, D K, Thirumalai, D

“…The nature of the nucleation-collapse mechanism in protein folding is probed using 27-mer and 36-mer lattice models. Three different forms for the interaction…”
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Stretching Single-Domain Proteins: Phase Diagram and Kinetics of Force-Induced Unfolding by Klimov, D. K., Thirumalai, D.

“…Single-molecule force spectroscopy reveals unfolding of domains in titin on stretching. We provide a theoretical framework for these experiments by computing…”
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Multiple stepwise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions by Li, Mai Suan, Hu, Chin-Kun, Klimov, Dmitri K, Thirumalai, D

“…Mechanical folding trajectories for polyproteins starting from initially stretched conformations generated by single-molecule atomic force microscopy…”
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Factors governing the foldability of proteins by Klimov, D. K., Thirumalai, D.

“…We use a three‐dimensional lattice model of proteins to investigate systematically the global properties of the polypeptide chains that determine the folding…”
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Progressing from folding trajectories to transition state ensemble in proteins by Klimov, D.K., Thirumalai, D.

“…A general procedure for determining the nature of the transition state ensemble (TSE) in proteins is used to probe the heterogeneity of TSE in two models of α/…”
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Lattice Model Studies of Force-Induced Unfolding of Proteins by Klimov, D. K, Thirumalai, D

“…We probe the general characteristics of force-induced unfolding of proteins using lattice models. The computations show that the experimental observations,…”
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