Free Energy, Entropy, and Induced Fit in Host−Guest Recognition:  Calculations with the Second-Generation Mining Minima Algorithm

2004 ◽  
Vol 126 (40) ◽  
pp. 13156-13164 ◽  
Author(s):  
Chia-En Chang ◽  
Michael K. Gilson
Keyword(s):  
Free Energy ◽  
Second Generation ◽  
Induced Fit ◽  
Energy Entropy ◽  
Mining Minima

Association/dissociation Mechanisms of Intrinsically Disordered Region of Protein Beyond Conformational Selection and Induced Fit

2019 ◽  
Author(s):  
Duy Phuoc Tran ◽  
Akio Kitao
Keyword(s):  
Free Energy ◽  
Transcriptional Activation ◽  
Binding Free Energy ◽  
Energy Structure ◽  
Induced Fit ◽  
Hydrogen Bond Formation ◽  
Conformational Selection ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Region ◽  
Dissociation Mechanisms

<p>We investigate association and dissociation mechanisms of a typical intrinsically disordered region (IDR), transcriptional activation subdomain of tumor repressor protein p53 (TAD-p53) with murine double-minute clone 2 protein (MDM2). Using the combination of cycles of association and dissociation parallel cascade molecular dynamics, multiple standard MD, and Markov state model, we are successful in obtaining the lowest free energy structure of MDM2/TAD-p53 complex as the structure very close to that in crystal without prior knowledge. This method also reproduces the experimentally measured standard binding free energy, and association and dissociation rate constants solely with the accumulated MD simulation cost of 11.675 μs, in spite of the fact that actual dissociation occurs in the order of a second. Although there exist a few complex intermediates with similar free energies, TAD-p53 first binds MDM2 as the second lowest free energy intermediate dominantly (> 90% in flux), taking a form similar to one of the intermediate structures in its monomeric state. The mechanism of this step has a feature of conformational selection. In the second step, dehydration of the interface, formation of π-π stackings of the side-chains, and main-chain relaxation/hydrogen bond formation to complete α-helix take place, showing features of induced fit. In addition, dehydration (dewetting) is a key process for the final relaxation around the complex interface. These results demonstrate a more fine-grained view of the IDR association/dissociation beyond classical views of protein conformational change upon binding.</p>

“Mining Minima”:  Direct Computation of Conformational Free Energy

1997 ◽  
Vol 101 (8) ◽  
pp. 1609-1618 ◽  
Author(s):  
Martha S. Head ◽  
James A. Given ◽  
Michael K. Gilson
Keyword(s):  
Free Energy ◽  
Direct Computation ◽  
Conformational Free Energy ◽  
Mining Minima

scholarly journals HIGH-TEMPERATURE FREE ENERGY, ENTROPY, ENTHALPY AND HEAT CAPACITY OF THORIUM SULFATE1

1960 ◽  
Vol 64 (7) ◽  
pp. 911-914 ◽  
Author(s):  
S. W. Mayer ◽  
B. B. Owens ◽  
T. H. Rutherford ◽  
R. B. Serrins
Keyword(s):  
Heat Capacity ◽  
Free Energy ◽  
High Temperature ◽  
Energy Entropy

scholarly journals Computational design of faster rotating second-generation light-driven molecular motors by control of steric effects

2015 ◽  
Vol 17 (33) ◽  
pp. 21740-21751 ◽  
Author(s):  
Baswanth Oruganti ◽  
Changfeng Fang ◽  
Bo Durbeej
Keyword(s):  
Free Energy ◽  
Molecular Motors ◽  
Energy Barrier ◽  
Second Generation ◽  
Molecular Motor ◽  
Computational Design ◽  
Steric Effects ◽  
Free Energy Barrier

By tuning the steric bulkiness of the stereogenic substituent, the rate-determining thermal free-energy barrier of an already MHz-capable rotary molecular motor can be reduced by a further 15–17 kJ mol−1.

scholarly journals Static and lattice vibrational energy differences between polymorphs

CrystEngComm ◽  
2015 ◽  
Vol 17 (28) ◽  
pp. 5154-5165 ◽  
Author(s):  
Jonas Nyman ◽  
Graeme M. Day
Keyword(s):  
Free Energy ◽  
Vibrational Energy ◽  
Lattice Energy ◽  
Energy Entropy

Lattice energy, entropy and free energy differences for over 500 pairs of known polymorphs are computed and discussed.

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