Probing Sequence Dependence of Folding Pathway of α-Helix Bundle Proteins through Free Energy Landscape Analysis

2014 ◽  
Vol 118 (22) ◽  
pp. 5891-5900 ◽  
Author(s):  
Qiang Shao
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Free Energy Landscape ◽  
Folding Pathway ◽  
Sequence Dependence ◽  
Helix Bundle ◽  
Α Helix

scholarly journals Multi-Funnel Landscape of the Fold-Switching Protein RfaH-CTD

2017 ◽  
Author(s):  
Nathan A. Bernhardt ◽  
Ulrich H.E. Hansmann
Keyword(s):  
Free Energy ◽  
Transcription Factor ◽  
Biological Function ◽  
Double Helix ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Conversion Process ◽  
Free Energy Landscape ◽  
Enhanced Sampling ◽  
Helix Bundle

AbstractProteins such as the transcription factor RfaH can change biological function by switching between distinct three-dimensional folds. RfaH regulates transcription if the C-terminal domain folds into a double helix bundle, and promotes translation when this domain assumes a β-barrel form. This fold-switch has been also observed for the isolated domain, dubbed by us RfaH-CTD, and is studied here with a variant of the RET approach recently introduced by us. We use the enhanced sampling properties of this technique to map the free energy landscape of RfaH-CTD and to propose a mechanism for the conversion process.TOC Image

Conformational modifications induced by internal tandem duplications on the FLT3 kinase and juxtamembrane domains

2019 ◽  
Vol 21 (34) ◽  
pp. 18467-18476 ◽  
Author(s):  
Guido Todde ◽  
Ran Friedman
Keyword(s):  
Free Energy ◽  
Protein Kinase ◽  
Molecular Dynamic ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Free Energy Landscape ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Tandem Duplications

FLT3 is a protein kinase that becomes aberrantly expressed in certain leukaemias. Insertions in the form of tandem duplications activate the protein and were studied by molecular dynamic simulations and free energy landscape analysis.

scholarly journals SOLVATION EFFECTS ON FREE ENERGY SURFACE OF POLYALANINE

2005 ◽  
Vol 16 (09) ◽  
pp. 1489-1496 ◽  
Author(s):  
GÖKHAN GÖKOĞLU ◽  
HANDAN ARKIN ◽  
ETHEM AKTÜRK ◽  
TARIK ÇELIK
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Solvent Effects ◽  
Energy Surface ◽  
Energy Landscape ◽  
Accessible Surface Area ◽  
Free Energy Landscape ◽  
Folding Pathway ◽  
Free Energy Surface ◽  
Accessible Surface

We have simulated 10-residue polyalanine chain by multicanonical method to visualize the 3D topographic picture of the free energy landscape over the whole range of temperatures, hence to show the funnel along the folding pathway exhaustively. We have simulated and compared the system in vacuo and in solvent, and examined the changes in the free energy landscape due to the solvent effects, which are taken into account by commonly used model Accessible Surface Area.

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