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Klaus Schulten - One of the best experts on this subject based on the ideXlab platform.
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fast Pressure Jump all atom simulations and experiments reveal site specific protein dehydration folding dynamics
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Maxim B Prigozhin, Martin Gruebele, Klaus Schulten, Yi Zhang, Taras V PogorelovAbstract:As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast Pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study Pressure-drop refolding of three λ-repressor fragment (λ6–85) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of Pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the nonperturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast Pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α3D)], whose drying and core formation proceed in concert, λ6–85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.
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observation of complete Pressure Jump protein refolding in molecular dynamics simulation and experiment
Journal of the American Chemical Society, 2014Co-Authors: Yanxin Liu, Maxim B Prigozhin, Klaus Schulten, Martin GruebeleAbstract:Density is an easily adjusted variable in molecular dynamics (MD) simulations. Thus, Pressure-Jump (P-Jump)-induced protein refolding, if it could be made fast enough, would be ideally suited for comparison with MD. Although Pressure denaturation perturbs secondary structure less than temperature denaturation, protein refolding after a fast P-Jump is not necessarily faster than that after a temperature Jump. Recent P-Jump refolding experiments on the helix bundle λ-repressor have shown evidence of a <3 μs burst phase, but also of a ∼1.5 ms “slow” phase of refolding, attributed to non-native helical structure frustrating microsecond refolding. Here we show that a λ-repressor mutant is nonetheless capable of refolding in a single explicit solvent MD trajectory in about 19 μs, indicating that the burst phase observed in experiments on the same mutant could produce native protein. The simulation reveals that after about 18.5 μs of conformational sampling, the productive structural rearrangement to the native state does not occur in a single swift step but is spread out over a brief series of helix and loop rearrangements that take about 0.9 μs. Our results support the molecular time scale inferred for λ-repressor from near-downhill folding experiments, where transition-state population can be seen experimentally, and also agrees with the transition-state transit time observed in slower folding proteins by single-molecule spectroscopy.
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fast protein refolding observed in Pressure Jump molecular dynamics simulation
Biophysical Journal, 2013Co-Authors: Yanxin Liu, Martin Gruebele, Klaus SchultenAbstract:Pressure Jump is known to induce fast protein folding. For a five-helix bundle λ-repressor fragment, a short refolding time of ∼2 μs was reported in an earlier Pressure-Jump experiment. To investigate this Pressure-Jump induced fast folding behavior, all-atom molecular dynamics simulations of more than 33 μs in explicit solvent were carried out on the same λ-repressor construct. High-Pressure denatured states, generated through a high-temperature unfolding and high-Pressure equilibration simulation procedure, were found to contain a significant amount of helical structure. Upon Pressure drop, the protein refolded into the native state in 20 μs. The folding in the simulation is slower than the one measured in Pressure-Jump experiment, but faster than the folding time of 80 μs measured in temperature-Jump experiment. A complete unfolding and refolding process was observed in the trajectory, which permitted the characterization of high-Pressure denatured states and refolding pathway. The Pressure Jump simulations carried out for this study can be employed in the future to investigate slow-folding proteins through 10∼100 μs molecular dynamics simulations by inducing a fast folding phase.
Martin Gruebele - One of the best experts on this subject based on the ideXlab platform.
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fast Pressure Jump all atom simulations and experiments reveal site specific protein dehydration folding dynamics
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Maxim B Prigozhin, Martin Gruebele, Klaus Schulten, Yi Zhang, Taras V PogorelovAbstract:As theory and experiment have shown, protein dehydration is a major contributor to protein folding. Dehydration upon folding can be characterized directly by all-atom simulations of fast Pressure drops, which create desolvated pockets inside the nascent hydrophobic core. Here, we study Pressure-drop refolding of three λ-repressor fragment (λ6–85) mutants computationally and experimentally. The three mutants report on tertiary structure formation via different fluorescent helix–helix contact pairs. All-atom simulations of Pressure drops capture refolding and unfolding of all three mutants by a similar mechanism, thus validating the nonperturbative nature of the fluorescent contact probes. Analysis of simulated interprobe distances shows that the α-helix 1–3 pair distance displays a slower characteristic time scale than the 1–2 or 3–2 pair distance. To see whether slow packing of α-helices 1 and 3 is reflected in the rate-limiting folding step, fast Pressure-drop relaxation experiments captured refolding on a millisecond time scale. These experiments reveal that refolding monitored by 1–3 contact formation indeed is much slower than when monitored by 1–2 or 3–2 contact formation. Unlike the case of the two-state folder [three–α-helix bundle (α3D)], whose drying and core formation proceed in concert, λ6–85 repeatedly dries and rewets different local tertiary contacts before finally forming a solvent-excluded core, explaining the non–two-state behavior observed during refolding in molecular dynamics simulations. This work demonstrates that proteins can explore desolvated pockets and dry globular states numerous times before reaching the native conformation.
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observation of complete Pressure Jump protein refolding in molecular dynamics simulation and experiment
Journal of the American Chemical Society, 2014Co-Authors: Yanxin Liu, Maxim B Prigozhin, Klaus Schulten, Martin GruebeleAbstract:Density is an easily adjusted variable in molecular dynamics (MD) simulations. Thus, Pressure-Jump (P-Jump)-induced protein refolding, if it could be made fast enough, would be ideally suited for comparison with MD. Although Pressure denaturation perturbs secondary structure less than temperature denaturation, protein refolding after a fast P-Jump is not necessarily faster than that after a temperature Jump. Recent P-Jump refolding experiments on the helix bundle λ-repressor have shown evidence of a <3 μs burst phase, but also of a ∼1.5 ms “slow” phase of refolding, attributed to non-native helical structure frustrating microsecond refolding. Here we show that a λ-repressor mutant is nonetheless capable of refolding in a single explicit solvent MD trajectory in about 19 μs, indicating that the burst phase observed in experiments on the same mutant could produce native protein. The simulation reveals that after about 18.5 μs of conformational sampling, the productive structural rearrangement to the native state does not occur in a single swift step but is spread out over a brief series of helix and loop rearrangements that take about 0.9 μs. Our results support the molecular time scale inferred for λ-repressor from near-downhill folding experiments, where transition-state population can be seen experimentally, and also agrees with the transition-state transit time observed in slower folding proteins by single-molecule spectroscopy.
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fast protein refolding observed in Pressure Jump molecular dynamics simulation
Biophysical Journal, 2013Co-Authors: Yanxin Liu, Martin Gruebele, Klaus SchultenAbstract:Pressure Jump is known to induce fast protein folding. For a five-helix bundle λ-repressor fragment, a short refolding time of ∼2 μs was reported in an earlier Pressure-Jump experiment. To investigate this Pressure-Jump induced fast folding behavior, all-atom molecular dynamics simulations of more than 33 μs in explicit solvent were carried out on the same λ-repressor construct. High-Pressure denatured states, generated through a high-temperature unfolding and high-Pressure equilibration simulation procedure, were found to contain a significant amount of helical structure. Upon Pressure drop, the protein refolded into the native state in 20 μs. The folding in the simulation is slower than the one measured in Pressure-Jump experiment, but faster than the folding time of 80 μs measured in temperature-Jump experiment. A complete unfolding and refolding process was observed in the trajectory, which permitted the characterization of high-Pressure denatured states and refolding pathway. The Pressure Jump simulations carried out for this study can be employed in the future to investigate slow-folding proteins through 10∼100 μs molecular dynamics simulations by inducing a fast folding phase.
Ad Bax - One of the best experts on this subject based on the ideXlab platform.
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observation of β amyloid peptide oligomerization by Pressure Jump nmr spectroscopy
Journal of the American Chemical Society, 2019Co-Authors: Ashley C Barnes, Philip A Anfinrud, Angus J Robertson, John M Louis, Ad BaxAbstract:Brain tissue of Alzheimer's disease patients invariably contains deposits of insoluble, fibrillar aggregates of peptide fragments of the amyloid precursor protein (APP), typically 40 or 42 residues in length and referred to as Aβ40 and Aβ42. However, it remains unclear whether these fibrils or oligomers constitute the toxic species. Depending on sample conditions, oligomers can form in a few seconds or less. These oligomers are invisible to solution NMR spectroscopy, but they can be rapidly ( 5 s) for residues 18-21 and 31-34, whereas the N-terminal 10 residues relax much faster (T1 ≤ 1.5 s), indicative of extensive internal motions. Transverse relaxation rates rapidly increase to ca. 1000 s-1 after the oligomerization is initiated.
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monitoring hydrogen exchange during protein folding by fast Pressure Jump nmr spectroscopy
Journal of the American Chemical Society, 2017Co-Authors: Reid T Alderson, Cyril Charlier, Philip A Anfinrud, Dennis A Torchia, Ad BaxAbstract:A method is introduced that permits direct observation of the rates at which backbone amide hydrogens become protected from solvent exchange after rapidly dropping the hydrostatic Pressure inside the NMR sample cell from denaturing (2.5 kbar) to native (1 bar) conditions. The method is demonstrated for a Pressure-sensitized ubiquitin variant that contains two Val to Ala mutations. Increased protection against hydrogen exchange with solvent is monitored as a function of time during the folding process. Results for 53 backbone amides show narrow clustering with protection occurring with a time constant of ca. 85 ms, but slower protection is observed around a reverse turn near the C-terminus of the protein. Remarkably, the native NMR spectrum returns with this slower time constant of ca. 150 ms, indicating that the almost fully folded protein retains molten globule characteristics with severe NMR line broadening until the final hydrogen bonds are formed. Prior to crossing the transition state barrier, hydrog...
Andro Mikelic - One of the best experts on this subject based on the ideXlab platform.
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Pressure Jump interface law for the stokes darcy coupling confirmation by direct numerical simulations
Journal of Fluid Mechanics, 2013Co-Authors: Thomas Carraro, Christian Goll, Anna Marciniakczochra, Andro MikelicAbstract:It is generally accepted that the effective velocity of a viscous flow over a porous bed satisfies the Beavers―Joseph slip law. To the contrary, the interface law for the effective stress has been a subject of controversy. Recently, a Pressure Jump interface law has been rigourously derived by Marciniak-Czochra and Mikelic. In this paper, we provide a confirmation of the analytical result using direct numerical simulation of the flow at the microscopic level. To the best of the authors' knowledge, this is the first numerical confirmation of the Pressure interface law in the literature.
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Pressure Jump interface law for the stokes darcy coupling confirmation by direct numerical simulations
arXiv: Numerical Analysis, 2013Co-Authors: Thomas Carraro, Christian Goll, Anna Marciniakczochra, Andro MikelicAbstract:It is generally accepted that the effective velocity of a viscous flow over a porous bed satisfies the Beavers-Joseph slip law. To the contrary, interface law for the effective stress has been a subject of controversy. Recently, a Pressure Jump interface law has been rigorously derived by Marciniak-Czochra and Mikeli\'c. In this paper, we provide a confirmation of the analytical result using direct numerical simulation of the flow at the microscopic level.
Yanxin Liu - One of the best experts on this subject based on the ideXlab platform.
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observation of complete Pressure Jump protein refolding in molecular dynamics simulation and experiment
Journal of the American Chemical Society, 2014Co-Authors: Yanxin Liu, Maxim B Prigozhin, Klaus Schulten, Martin GruebeleAbstract:Density is an easily adjusted variable in molecular dynamics (MD) simulations. Thus, Pressure-Jump (P-Jump)-induced protein refolding, if it could be made fast enough, would be ideally suited for comparison with MD. Although Pressure denaturation perturbs secondary structure less than temperature denaturation, protein refolding after a fast P-Jump is not necessarily faster than that after a temperature Jump. Recent P-Jump refolding experiments on the helix bundle λ-repressor have shown evidence of a <3 μs burst phase, but also of a ∼1.5 ms “slow” phase of refolding, attributed to non-native helical structure frustrating microsecond refolding. Here we show that a λ-repressor mutant is nonetheless capable of refolding in a single explicit solvent MD trajectory in about 19 μs, indicating that the burst phase observed in experiments on the same mutant could produce native protein. The simulation reveals that after about 18.5 μs of conformational sampling, the productive structural rearrangement to the native state does not occur in a single swift step but is spread out over a brief series of helix and loop rearrangements that take about 0.9 μs. Our results support the molecular time scale inferred for λ-repressor from near-downhill folding experiments, where transition-state population can be seen experimentally, and also agrees with the transition-state transit time observed in slower folding proteins by single-molecule spectroscopy.
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fast protein refolding observed in Pressure Jump molecular dynamics simulation
Biophysical Journal, 2013Co-Authors: Yanxin Liu, Martin Gruebele, Klaus SchultenAbstract:Pressure Jump is known to induce fast protein folding. For a five-helix bundle λ-repressor fragment, a short refolding time of ∼2 μs was reported in an earlier Pressure-Jump experiment. To investigate this Pressure-Jump induced fast folding behavior, all-atom molecular dynamics simulations of more than 33 μs in explicit solvent were carried out on the same λ-repressor construct. High-Pressure denatured states, generated through a high-temperature unfolding and high-Pressure equilibration simulation procedure, were found to contain a significant amount of helical structure. Upon Pressure drop, the protein refolded into the native state in 20 μs. The folding in the simulation is slower than the one measured in Pressure-Jump experiment, but faster than the folding time of 80 μs measured in temperature-Jump experiment. A complete unfolding and refolding process was observed in the trajectory, which permitted the characterization of high-Pressure denatured states and refolding pathway. The Pressure Jump simulations carried out for this study can be employed in the future to investigate slow-folding proteins through 10∼100 μs molecular dynamics simulations by inducing a fast folding phase.
