Free Energy Contribution Analysis Using Response Kernel Approximation: Insights into the Acylation Reaction of a Beta-Lactamase

2016 ◽  
Vol 120 (35) ◽  
pp. 9338-9346 ◽  
Author(s):  
Toshio Asada ◽  
Kanta Ando ◽  
Pradipta Bandyopadhyay ◽  
Shiro Koseki
Keyword(s):  
Free Energy ◽  
Beta Lactamase ◽  
Energy Contribution ◽  
Acylation Reaction ◽  
Kernel Approximation ◽  
Contribution Analysis ◽  
Free Energy Contribution

scholarly journals Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin

2008 ◽  
Vol 5 (29) ◽  
pp. 1391-1408 ◽  
Author(s):  
Gabriel M Altschuler ◽  
Keith R Willison
Keyword(s):  
Free Energy ◽  
Essential Role ◽  
Cytoskeletal Protein ◽  
Type I ◽  
Folding Intermediate ◽  
Energy Contribution ◽  
Nucleotide Hydrolysis ◽  
Chaperonin Groel ◽  
Free Energy Contribution ◽  
Bacterial Type

A free-energy-based approach is used to describe the mechanism through which chaperonin-containing TCP-1 (CCT) folds the filament-forming cytoskeletal protein actin, which is one of its primary substrates. The experimental observations on the actin folding and unfolding pathways are collated and then re-examined from this perspective, allowing us to determine the position of the CCT intervention on the actin free-energy folding landscape. The essential role for CCT in actin folding is to provide a free-energy contribution from its ATP cycle, which drives actin to fold from a stable, trapped intermediate I 3 , to a less stable but now productive folding intermediate I 2 . We develop two hypothetical mechanisms for actin folding founded upon concepts established for the bacterial type I chaperonin GroEL and extend them to the much more complex CCT system of eukaryotes. A new model is presented in which CCT facilitates free-energy transfer through direct coupling of the nucleotide hydrolysis cycle to the phases of actin substrate maturation.

Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes

2004 ◽  
Vol 47 (18) ◽  
pp. 4507-4516 ◽  
Author(s):  
Micaela Fornabaio ◽  
Francesca Spyrakis ◽  
Andrea Mozzarelli ◽  
Pietro Cozzini ◽  
Donald J. Abraham ◽  
...  
Keyword(s):  
Free Energy ◽  
Water Molecules ◽  
Energy Contribution ◽  
Structural Water ◽  
Free Energy Contribution ◽  
Free Energy Of Binding ◽  
Hiv 1

The mechanism and conformational changes of polybrominated diphenyl ethers to TTR by fluorescence spectroscopy, molecular simulation, and quantum chemistry

The Analyst ◽  
2018 ◽  
Vol 143 (19) ◽  
pp. 4662-4673
Author(s):  
Jie Xu ◽  
Yuchen Wei ◽  
Wu Yang ◽  
Lulu Yang ◽  
Zhongsheng Yi
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Molecular Modeling ◽  
Fluorescence Spectroscopy ◽  
Quantum Chemistry ◽  
Conformational Changes ◽  
Polybrominated Diphenyl Ethers ◽  
Energy Contribution ◽  
Diphenyl Ethers ◽  
Free Energy Contribution

Free energy contribution of amino acid LYS (B and D chains) and PDBEs was analyzed combining quantum chemistry and molecular modeling.

scholarly journals Improved Model for Predicting the Free Energy Contribution of Dinucleotide Bulges to RNA Duplex Stability

Biochemistry ◽  
2015 ◽  
Vol 54 (34) ◽  
pp. 5290-5296 ◽  
Author(s):  
Jeremy C. Tomcho ◽  
Magdalena R. Tillman ◽  
Brent M. Znosko
Keyword(s):  
Free Energy ◽  
Energy Contribution ◽  
Duplex Stability ◽  
Improved Model ◽  
Free Energy Contribution

scholarly journals Improved Model to Predict the Free Energy Contribution of Trinucleotide Bulges to RNA Duplex Stability

Biochemistry ◽  
2014 ◽  
Vol 53 (21) ◽  
pp. 3502-3508 ◽  
Author(s):  
Meghan H. Murray ◽  
Jessicah A. Hard ◽  
Brent M. Znosko
Keyword(s):  
Free Energy ◽  
Energy Contribution ◽  
Duplex Stability ◽  
Improved Model ◽  
Free Energy Contribution
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