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Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape
(Cell Press, 2016-07-26)
Protein folding is a central problem in biological physics. Energetic roughness is an important aspect that controls protein-folding stability and kinetics. The roughness is associated with conflicting interactions in the ...
Artificial Itelligence Teaches Drugs to Target Proteins by Tackling the Induced Folding Problem
(American Chemical Society, 2020-06-17)
We explore the possibility of a deep learning (DL) platform that steers drug design to target proteins by inducing binding-competent conformations. We deal with the fact that target proteins are usually not fixed targets ...
Thioredoxin from Escherichia coli as a role model of molecular recognition, folding, dynamics and function
(Bentham Science Publishers, 2015-09)
Thioredoxin (TRX) catalyzes redox reactions via the reversible oxidation of the conserved active center CGPC and it is involved in multiple biological processes, some of them linked to redox activity while others not. TRX ...
Coordinate and time-dependent diffusion dynamics in protein folding
(Academic Press Inc. Elsevier B.V., 2010-09-01)
We developed both analytical and simulation methods to explore the diffusion dynamics in protein folding. We found the diffusion as a quantitative measure of escape from local traps along the protein folding funnel with ...
Coordinate and time-dependent diffusion dynamics in protein folding
(Academic Press Inc. Elsevier B.V., 2010-09-01)
We developed both analytical and simulation methods to explore the diffusion dynamics in protein folding. We found the diffusion as a quantitative measure of escape from local traps along the protein folding funnel with ...
Folding of a dimeric β-barrel: Residual structure in the urea denatured state of the human papillomavirus E2 DNA binding domain
(Cambridge University Press, 2000-04)
The dimeric beta-barrel is a characteristic topology initially found in the transcriptional regulatory domain of the E2 DNA binding domain from papillomaviruses. We have previously described the kinetic folding mechanism ...
The Design of Repeat Proteins: Stability Conflicts with Functionality
(Insight Medical Publishing, 2017-03)
Repeat proteins are constituted by a variable number of copies of a given structural element that is tandemly repeated along a longitudinal axis. They mainly function as protein-protein interactors with binding interfaces ...
The principle of minimal episteric distortion of the water matrix and its role in protein folding
(American Institute Of Physics, 2013-08)
A significant episteric (around a solid) distortion of the hydrogen-bond structure of water is promoted by solutes with nanoscale surface detail and physico-chemical complexity, such as soluble natural proteins. These ...
Equilibrium partially folded states of B. licheniformis β -lactamase
(Springer, 2019-03-30)
훽-Lactamases (penicillinases) facilitate bacterial resistance to antibiotics and are excellent theoretical and experimental models in protein structure, dynamics and evolution. Bacillus licheniformis exo-small penicillinase ...