The effects of implicit modeling of nonpolar solvation on protein folding simulations

2018 ◽  
Vol 20 (27) ◽  
pp. 18410-18419 ◽  
Author(s):  
Qiang Shao ◽  
Weiliang Zhu
Keyword(s):  
Surface Tension ◽  
Protein Folding ◽  
Helix Bundle ◽  
Implicit Modeling ◽  
Folding Simulations ◽  
Α Helix ◽  
Nonpolar Solvation ◽  
Surface Tension Coefficients

Folding simulations of β-hairpin and α-helix bundle proteins with varied surface tension coefficients embedded in a popular SA model were performed to reveal the effects of implicit modeling of nonpolar solvation on protein folding.

FOLDING SIMULATIONS FOR A THREE-HELIX BUNDLE PROTEIN

2003 ◽  
Vol 17 (01n02) ◽  
pp. 49-54 ◽  
Author(s):  
LONGHUA HU ◽  
JUN WANG ◽  
WEI WANG
Keyword(s):  
Protein Folding ◽  
Dihedral Angle ◽  
Lattice Model ◽  
Helix Bundle ◽  
Thermodynamics And Kinetics ◽  
Wide Range ◽  
Folding Simulations ◽  
Kinetics Of ◽  
Folding Thermodynamics ◽  
Bundle Protein

The folding thermodynamics and kinetics of a three-helix bundle protein with off-lattice model are studied using Monter Carlo simulations over a wide range of temperatures. By varying the strength of the dihedral angle potential, the effect of dihedral angle in folding is examined and it is demonstrated that the dihedral angle potential has much influence on protein folding thermodynamics and kinetics.

De NovoDesign and Synthesis of Four α-Helix Bundle Proteins with Flavin Function

1993 ◽  
Vol 22 (9) ◽  
pp. 1533-1536 ◽  
Author(s):  
Hisakazu Mihara ◽  
Kin-ya Tomizaki ◽  
Norikazu Nishino ◽  
Tsutomu Fujimoto
Keyword(s):  
Helix Bundle ◽  
Α Helix

scholarly journals Deciphering molecular details of the RAC–ribosome interaction by EPR spectroscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sandra J. Fries ◽  
Theresa S. Braun ◽  
Christoph Globisch ◽  
Christine Peter ◽  
Malte Drescher ◽  
...  
Keyword(s):  
Protein Folding ◽  
Epr Spectroscopy ◽  
De Novo ◽  
Contact Point ◽  
Ribosomal Subunit ◽  
Paramagnetic Resonance ◽  
40S Ribosomal Subunit ◽  
Site Directed Spin Labeling ◽  
Α Helix ◽  
Chaperone Complex

AbstractThe eukaryotic ribosome-associated complex (RAC) plays a significant role in de novo protein folding. Its unique interaction with the ribosome, comprising contacts to both ribosomal subunits, suggests a RAC-mediated coordination between translation elongation and co-translational protein folding. Here, we apply electron paramagnetic resonance (EPR) spectroscopy combined with site-directed spin labeling (SDSL) to gain deeper insights into a RAC–ribosome contact affecting translational accuracy. We identified a local contact point of RAC to the ribosome. The data provide the first experimental evidence for the existence of a four-helix bundle as well as a long α-helix in full-length RAC, in solution as well as on the ribosome. Additionally, we complemented the structural picture of the region mediating this functionally important contact on the 40S ribosomal subunit. In sum, this study constitutes the first application of SDSL-EPR spectroscopy to elucidate the molecular details of the interaction between the 3.3 MDa translation machinery and a chaperone complex.

scholarly journals Deep clustering of protein folding simulations

2018 ◽  
Vol 19 (S18) ◽  
Author(s):  
Debsindhu Bhowmik ◽  
Shang Gao ◽  
Michael T. Young ◽  
Arvind Ramanathan
Keyword(s):  
Protein Folding ◽  
Folding Simulations

scholarly journals Protein Evolution across Fold Classes: A 3-α-Helix Bundle can Switch to β, α/β, and α+β Folds by Stepwise Mutation

2015 ◽  
Vol 108 (2) ◽  
pp. 203a-204a
Author(s):  
Lauren L. Porter ◽  
Yanan He ◽  
Yihong Chen ◽  
John Orban ◽  
Philip N. Bryan
Keyword(s):  
Protein Evolution ◽  
Helix Bundle ◽  
Stepwise Mutation ◽  
Α Helix
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