The Experts below are selected from a list of 64347 Experts worldwide ranked by ideXlab platform
Ziv Reich - One of the best experts on this subject based on the ideXlab platform.
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Protein Energy Landscape roughness.
Biochemical Society transactions, 2008Co-Authors: Ruti Kapon, Reinat Nevo, Ziv ReichAbstract:The 'new view' of proteins sees protein reactions as parallel processes occurring along funnelled Energy Landscapes. These Landscapes are generally not smooth, but are superimposed by hills and valleys of different heights and widths leading to roughness on the Energy surface. In the present paper, we describe the origins of protein Energy Landscape roughness, measurements of its scale and its implications.
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direct measurement of protein Energy Landscape roughness
EMBO Reports, 2005Co-Authors: Reina Nevo, Vlad Umfeld, Ruti Kapo, Pete Hinterdorfe, Ziv ReichAbstract:The Energy Landscape of proteins is thought to have an intricate, corrugated structure. Such roughness should have important consequences on the folding and binding kinetics of proteins, as well as on their equilibrium fluctuations. So far, no direct measurement of protein Energy Landscape roughness has been made. Here, we combined a recent theory with single‐molecule dynamic force spectroscopy experiments to extract the overall Energy scale of roughness e for a complex consisting of the small GTPase Ran and the nuclear transport receptor importin‐β. The results gave e >5 k B T , indicating a bumpy Energy surface, which is consistent with the ability of importin‐β to accommodate multiple conformations and to interact with different, structurally distinct ligands.
Martin Gruebele - One of the best experts on this subject based on the ideXlab platform.
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Exploring the Energy Landscape of a small RNA hairpin.
Journal of the American Chemical Society, 2006Co-Authors: David J. Proctor, Elzbieta Kierzek, Ryszard Kierzek, Philip C. Bevilacqua, Martin GruebeleAbstract:The Energy Landscape of a small RNA tetraloop hairpin is explored by temperature jump kinetics and base-substitution. The folding kinetics are single-exponential near the folding transition midpoint T(m). An additional fast phase appears below the midpoint, and an additional slow phase appears above the midpoint. Stem mutation affects the high-temperature phase, while loop mutation affects the low-temperature phase. An adjusted 2-D lattice model reproduces the temperature-dependent phases, although it oversimplifies the structural interpretation. A four-state free Energy Landscape model is generated based on the lattice model. This model explains the thermodynamics and multiphase kinetics over the full temperature range of the experiments. An analysis of three variants shows that one of the intermediate RNA structures is a stacking-related trap affected by stem but not loop modification, while the other is an early intermediate that forms some stem and loop structure. Even a very fast-folding 8-mer RNA with an ideal tetraloop sequence has a rugged Energy Landscape, ideal for testing analytical and computational models.
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exploring the Energy Landscape of a small rna hairpin
Journal of the American Chemical Society, 2006Co-Authors: David J. Proctor, Elzbieta Kierzek, Ryszard Kierzek, Philip C. Bevilacqua, Martin GruebeleAbstract:The Energy Landscape of a small RNA tetraloop hairpin is explored by temperature jump kinetics and base-substitution. The folding kinetics are single-exponential near the folding transition midpoint Tm. An additional fast phase appears below the midpoint, and an additional slow phase appears above the midpoint. Stem mutation affects the high-temperature phase, while loop mutation affects the low-temperature phase. An adjusted 2-D lattice model reproduces the temperature-dependent phases, although it oversimplifies the structural interpretation. A four-state free Energy Landscape model is generated based on the lattice model. This model explains the thermodynamics and multiphase kinetics over the full temperature range of the experiments. An analysis of three variants shows that one of the intermediate RNA structures is a stacking-related trap affected by stem but not loop modification, while the other is an early intermediate that forms some stem and loop structure. Even a very fast-folding 8-mer RNA with...
Tristan Bereau - One of the best experts on this subject based on the ideXlab platform.
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Free-Energy Landscape of polymer-crystal polymorphism.
Soft matter, 2020Co-Authors: Chan Liu, Jan Gerit Brandenburg, Omar Valsson, Kurt Kremer, Tristan BereauAbstract:Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-Energy Landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the first time the free-Energy Landscape of a polymorphic crystalline polymer, syndiotactic polystyrene. Coarse-grained metadynamics simulations allow us to efficiently sample the Landscape at large. The free-Energy difference between the two main polymorphs, α and β, is further investigated by quantum-chemical calculations. The results of the two methods are in line with experimental observations: they predict β as the more stable polymorph under standard conditions. Critically, the free-Energy Landscape suggests how the α polymorph may lead to experimentally observed kinetic traps. The combination of multiscale modeling, enhanced sampling, and quantum-chemical calculations offers an appealing strategy to uncover complex free-Energy Landscapes with polymorphic behavior.
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Free-Energy Landscape of polymer-crystal polymorphism.
arXiv: Soft Condensed Matter, 2020Co-Authors: Chan Liu, Jan Gerit Brandenburg, Omar Valsson, Kurt Kremer, Tristan BereauAbstract:Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-Energy Landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the first time the free-Energy Landscape of a polymorphic crystalline polymer, syndiotactic polystyrene. Coarse-grained metadynamics simulations allow us to efficiently sample the Landscape at large. The free-Energy difference between the two main polymorphs, $\alpha$ and $\beta$, is further investigated by quantum-chemical calculations. The two methods are in line with experimental observations: they predict $\beta$ as the more stable polymorph at standard conditions. Critically, the free-Energy Landscape suggests how the $\alpha$ polymorph may lead to experimentally observed kinetic traps. The combination of multiscale modeling, enhanced sampling, and quantum-chemical calculations offers an appealing strategy to uncover complex free-Energy Landscapes with polymorphic behavior.
Anatoliy Senyshyn - One of the best experts on this subject based on the ideXlab platform.
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Superionic Diffusion through Frustrated Energy Landscape
Chem, 2019Co-Authors: Davide Di Stefano, M Lechartier, Anna Miglio, Yaroslav Filinchuk, Anatoliy Senyshyn, Koen Robeyns, Hiroyuki Ishida, Stefan Spannenberger, Denise Prutsch, Sarah LunghammerAbstract:Summary Solid-state materials with high ionic conduction are necessary for many technologies, including all-solid-state lithium (Li)-ion batteries. Understanding how crystal structure dictates ionic diffusion is at the root of the development of fast ionic conductors. Here, we show that LiTi2(PS4)3 exhibits a Li-ion diffusion coefficient about an order of magnitude higher than that of current state-of-the-art Li superionic conductors. We rationalize this observation by the unusual crystal structure of LiTi2(PS4)3, which offers no regular tetrahedral or octahedral sites for Li to favorably occupy. This creates a smooth, frustrated Energy Landscape resembling the Energy Landscapes present in liquids more than those in typical solids. This frustrated Energy Landscape leads to a high diffusion coefficient, combining low activation Energy with a high pre-factor.
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Superionic diffusion through frustrated Energy Landscape
arXiv.org, 2017Co-Authors: D Di Stefano, M Lechartier, Anna Miglio, Yaroslav Filinchuk, Koen Robeyns, Anatoliy SenyshynAbstract:Solid-state materials with extremely high ionic diffusion are necessary to many technologies including all-solid-state Li-ion batteries. In this work, we demonstrate through experimental characterization and theoretical analysis that LiTi2(PS4)3 or LTPS shows exceptional Li-ion diffusion, an order of magnitude higher than current state-of-the-art superionic conductors. We propose a rationalization to this behavior by the frustrated Energy Landscape experienced by lithium ions in the LTPS framework. LTPS shows a unique crystal structure with no regular tetrahedral or octahedral sites for lithium to favorably occupy. This leads to a smooth Energy Landscape combining small Energy barriers with numerous diffusion paths. This Energy Landscape is closer to a liquid than typical crystalline solids and is at the root of the exceptional diffusion behavior in LTPS. The concept of a crystalline framework with frustrated Energy Landscape offers an entirely new design principle to guide the search of future high performance superionic conductors.
Matthias Rief - One of the best experts on this subject based on the ideXlab platform.
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full distance resolved folding Energy Landscape of one single protein molecule
Proceedings of the National Academy of Sciences of the United States of America, 2010Co-Authors: Christof J M Gebhardt, Thomas Bornschlogl, Matthias RiefAbstract:Kinetic bulk and single molecule folding experiments characterize barrier properties but the shape of folding Landscapes between barrier top and native state is difficult to access. Here, we directly extract the full free Energy Landscape of a single molecule of the GCN4 leucine zipper using dual beam optical tweezers. To this end, we use deconvolution force spectroscopy to follow an individual molecule’s trajectory with high temporal and spatial resolution. We find a heterogeneous Energy Landscape of the GCN4 leucine zipper domain. The Energy profile is divided into two stable C-terminal heptad repeats and two less stable repeats at the N-terminus. Energies and transition barrier positions were confirmed by single molecule kinetic analysis. We anticipate that deconvolution sampling is a powerful tool for the model-free investigation of protein Energy Landscapes.
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exploring the Energy Landscape of gfp by single molecule mechanical experiments
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Hendrik Dietz, Matthias RiefAbstract:We use single-molecule force spectroscopy to drive single GFP molecules from the native state through their complex Energy Landscape into the completely unfolded state. Unlike many smaller proteins, mechanical GFP unfolding proceeds by means of two subsequent intermediate states. The transition from the native state to the first intermediate state occurs near thermal equilibrium at ≈35 pN and is characterized by detachment of a seven-residue N-terminal α-helix from the beta barrel. We measure the equilibrium free Energy cost associated with this transition as 22 kBT. Detachment of this small α-helix completely destabilizes GFP thermodynamically even though the β-barrel is still intact and can bear load. Mechanical stability of the protein on the millisecond timescale, however, is determined by the activation barrier of unfolding the β-barrel out of this thermodynamically unstable intermediate state. High bandwidth, time-resolved measurements of the cantilever relaxation phase upon unfolding of the β-barrel revealed a second metastable mechanical intermediate with one complete β-strand detached from the barrel. Quantitative analysis of force distributions and lifetimes lead to a detailed picture of the complex mechanical unfolding pathway through a rough Energy Landscape.
