Collapse Transition
Mostrando 13-24 de 44 artigos, teses e dissertações.
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13. Drying-induced hydrophobic polymer collapse
We have used computer simulation to study the collapse of a hydrophobic chain in water. We find that the mechanism of collapse is much like that of a first-order phase transition. The evaporation of water in the vicinity of the polymer provides the driving force for collapse, and the rate limiting step is the nucleation of a sufficiently large vapor bubble.
The National Academy of Sciences.
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14. How fast is protein hydrophobic collapse?
One of the most recurring questions in protein folding refers to the interplay between formation of secondary structure and hydrophobic collapse. In contrast with secondary structure, it is hard to isolate hydrophobic collapse from other folding events. We have directly measured the dynamics of protein hydrophobic collapse in the absence of competing process
National Academy of Sciences.
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15. Kinetics and thermodynamics of folding in model proteins.
Monte Carlo simulations on a class of lattice models are used to probe the thermodynamics and kinetics of protein folding. We find two transition temperatures: one at T theta, when chains collapse from a coil to a compact phase, and the other at Tf (< T theta), when chains adopt a conformation corresponding to their native state. The kinetics are probed by s
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16. Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding.
The equilibrium and kinetics of folding of the single-domain protein chymotrypsin inhibitor 2 conform to the simple two-state model. The structure of the rate-determining transition state has been mapped out at the resolution of individual side chains by using the protein engineering method on 74 mutants that have been constructed at 37 of the 64 residues. T
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17. Folding thermodynamics of a model three-helix-bundle protein
The calculated folding thermodynamics of a simple off-lattice three-helix-bundle protein model under equilibrium conditions shows the experimentally observed protein transitions: a collapse transition, a disordered-to-ordered globule transition, a globule to native-state transition, and the transition from the active native state to a frozen inactive state.
The National Academy of Sciences of the USA.
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18. Transition-path sampling of β-hairpin folding
We examine the dynamical folding pathways of the C-terminal β-hairpin of protein G-B1 in explicit solvent at room temperature by means of a transition-path sampling algorithm. In agreement with previous free-energy calculations, the resulting path ensembles reveal a folding mechanism in which the hydrophobic residues collapse first followed by backbone hydr
National Academy of Sciences.
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19. A Transition to a Compact Form of DNA in Polymer Solutions
In the presence of over-threshold concentrations of simple neutral polymers and salts, DNA undergoes a cooperative change in its solution structure. Sedimentation studies at low DNA concentrations show that phage DNA molecules collapse into particles approaching the compactness of the contents of phage heads. The interaction between DNA and polymers is thoug
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20. Monte Carlo simulations on an equilibrium globular protein folding model.
Monte Carlo simulations were performed on a diamond lattice, globular protein model in which the trans conformational state is energetically favored over the gauche states (thereby perhaps favoring a beta-sheet secondary structure) and in which nonspecific nonbonded nearest-neighbor attractive interactions are allowed. If the attractive interactions are suff
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21. Tris-borate is a poor counterion for RNA: a cautionary tale for RNA folding studies
Native polyacrylamide gel electrophoresis is a powerful approach for visualizing RNA folding states and folding intermediates. Tris-borate has a high-buffering capacity and is therefore widely used in electrophoresis-based investigations of RNA structure and folding. However, the effectiveness of Tris-borate as a counterion for RNA has not been systematicall
Oxford University Press.
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22. Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funn
The National Academy of Sciences.
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23. Exploring the folding free energy surface of a three-helix bundle protein
The multidimensional free energy surface for a small fast folding helical protein is explored based on first-principle calculations. The model represents the 46-residue segment from fragment B of staphylococcal protein A. The relationship between collapse and tertiary structure formation, and the order of collapse and secondary structure formation, are inves
The National Academy of Sciences of the USA.
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24. Vertical collapse of a cytolysin prepore moves its transmembrane β-hairpins to the membrane
Perfringolysin O (PFO) is a prototype of the large family of pore-forming cholesterol-dependent cytolysins (CDCs). A central enigma of the cytolytic mechanism of the CDCs is that their membrane-spanning β-hairpins (the transmembrane amphipathic β-hairpins (TMHs)) appear to be ∼40 Å too far above the membrane surface to cross the bilayer and form the por
Nature Publishing Group.