scholarly journals Structure, Thermodynamics, and Folding Pathways for a Tryptophan Zipper as a Function of Local Rigidification

2016 ◽  
Vol 12 (12) ◽  
pp. 6109-6117 ◽  
Author(s):  
Jerelle A. Joseph ◽  
Chris S. Whittleston ◽  
David J. Wales
Keyword(s):  
Folding Pathways ◽  
Tryptophan Zipper

scholarly journals Co-self-assembly of multiple DNA origami nanostructures in a single pot

2021 ◽  
Author(s):  
Joshua A. Johnson ◽  
Vasiliki Kolliopoulos ◽  
Carlos E. Castro
Keyword(s):  
Self Assembly ◽  
Dna Origami ◽  
Folding Pathways

We demonstrate co-self-assembly of two distinct DNA origami structures with a common scaffold strand through programmable bifurcation of folding pathways.

scholarly journals Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR

Biology ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 656
Author(s):  
Vincent Van Deuren ◽  
Yin-Shan Yang ◽  
Karine de Guillen ◽  
Cécile Dubois ◽  
Catherine Anne Royer ◽  
...  
Keyword(s):  
High Pressure ◽  
Staphylococcal Nuclease ◽  
Comparative Assessment ◽  
Side Chain ◽  
Folding Pathway ◽  
Hydrophobic Core ◽  
Folding Pathways ◽  
Partial Unfolding ◽  
Protein Folding Pathways ◽  
Similar Description

Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CH groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CH, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CH when compared to amide groups.

Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein

2021 ◽  
Vol 143 (3) ◽  
pp. 1447-1457
Author(s):  
Sandhya Bhatia ◽  
Guruswamy Krishnamoorthy ◽  
Jayant B. Udgaonkar
Keyword(s):  
Structure Formation ◽  
Small Protein ◽  
Folding Pathways

Oligomeric States along the Folding Pathways of β2-Microglobulin: Kinetics, Thermodynamics, and Structure

2013 ◽  
Vol 425 (15) ◽  
pp. 2722-2736 ◽  
Author(s):  
E. Rennella ◽  
T. Cutuil ◽  
P. Schanda ◽  
I. Ayala ◽  
F. Gabel ◽  
...  
Keyword(s):  
Β2 Microglobulin ◽  
Folding Pathways

Self-consistent calculation of protein folding pathways

2017 ◽  
Vol 147 (6) ◽  
pp. 064108 ◽  
Author(s):  
S. Orioli ◽  
S. a Beccara ◽  
P. Faccioli
Keyword(s):  
Protein Folding ◽  
Consistent Calculation ◽  
Self Consistent ◽  
Folding Pathways ◽  
Protein Folding Pathways

Models of cooperativity in protein folding

1995 ◽  
Vol 348 (1323) ◽  
pp. 61-70 ◽  
Keyword(s):  
Protein Folding ◽  
Molten Globule ◽  
Core Collapse ◽  
Hydrophobic Core ◽  
Model Studies ◽  
Helix Formation ◽  
Collapse Model ◽  
Folding Pathways ◽  
State Behaviour ◽  
Denatured States

What is the basis for the two-state cooperativity of protein folding? Since the 1950s, three main models have been put forward. 1. In ‘helix-coil’ theory, cooperativity is due to local interactions among near neighbours in the sequence. Helix-coil cooperativity is probably not the principal basis for the folding of globular proteins because it is not two-state, the forces are weak, it does not account for sheet proteins, and there is no evidence that helix formation precedes the formation of a hydrophobic core in the folding pathways. 2. In the ‘sidechain packing’ model, cooperativity is attributed to the jigsaw-puzzle-like complementary fits of sidechains. This too is probably not the basis of folding cooperativity because exact models and experiments on homopolymers with sidechains give no evidence that sidechain freezing is two-state, sidechain complementarities in proteins are only weak trends, and the molten globule model predicted by this model is far more native-like than experiments indicate. 3. In the ‘hydrophobic core collapse’ model, cooperativity is due to the assembly of non-polar residues into a good core. Exact model studies show that this model gives two-state behaviour for some sequences of hydrophobic and polar monomers. It is based on strong forces. There is considerable experimental evidence for the kinetics this model predicts: the development of hydrophobic clusters and cores is concurrent with secondary structure formation. It predicts compact denatured states with sizes and degrees of disorder that are in reasonable agreement with experiments.

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