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Analyzing the effect of homogeneous frustration in protein folding
(2013-10-01)
The energy landscape theory has been an invaluable theoretical framework in the understanding of biological processes such as protein folding, oligomerization, and functional transitions. According to the theory, the energy ...
Detailing Protein Landscapes under Pressure
(Cell Press, 2016-12)
Natural protein molecules are remarkablephysical objects. Despite the astronomicalnumber of competing structuralforms, these systems self-organize intobeautiful structural ensembles in biologicallyshort timescales, puzzlingout ...
Specific and nonspecific collapse in protein folding funnels
(2002-04-22)
Experiments with fast folding proteins are beginning to address the relationship between collapse and folding. We investigate how different scenarios for folding can arise depending on whether the folding and collapse ...
Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure
(Wiley-Blackwell, 2014-07-01)
The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as ...
Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin
(SPRINGERNEW YORK, 2012)
Molecular dynamics simulations of the model protein chignolin with explicit solvent were carried out, in order to analyze the influence of the Berendsen thermostat on the evolution and folding of the peptide. The dependence ...
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 ...
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 ...
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 ...