scholarly journals Kinetic Evidence for an Induced-Fit Mechanism in the Binding of the Substrate Camphor by Cytochrome P450cam

ACS Catalysis ◽  
2020 ◽  
pp. 639-649
Author(s):  
F. Peter Guengerich ◽  
Stella A. Child ◽  
Ian R. Barckhausen ◽  
Margo H. Goldfarb
Keyword(s):  
Cytochrome P450cam ◽  
Induced Fit

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>

'Induced Fit-Lock and Key' Model in Enzymic Reactions*

2011 ◽  
Vol 38 (5) ◽  
pp. 418-426 ◽  
Author(s):  
Zi-Jian ZHANG ◽  
Rong PAN ◽  
Yuan ZHOU ◽  
Rong-Qiao HE
Keyword(s):  
Induced Fit

Reverse Induced Fit-Driven MAS-Downstream Transduction: Looking for Metabotropic Agonists

2017 ◽  
Vol 24 (39) ◽  
Author(s):  
Larissa Pernomian ◽  
Mayara S. Gomes ◽  
Carlos H. Tomich de Paula da Silva ◽  
Joaquin M.C. Rosa
Keyword(s):  
Induced Fit

From Selection to Instruction and Back — Competing Conformational Selection and Induced Fit Pathways in Abiotic Hosts

2021 ◽  
Author(s):  
Jovica D Badjic ◽  
Radoslav Z Pavlović ◽  
Remy F Lalisse ◽  
Alexandar L Hansen ◽  
Christopher A Waudby ◽  
...  
Keyword(s):  
Induced Fit ◽  
Conformational Selection

scholarly journals Structural and Kinetic Studies of Induced Fit in Xylulose Kinase from Escherichia coli

2007 ◽  
Vol 365 (3) ◽  
pp. 783-798 ◽  
Author(s):  
Eric Di Luccio ◽  
Barbara Petschacher ◽  
Jennifer Voegtli ◽  
Hui-Ting Chou ◽  
Henning Stahlberg ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Kinetic Studies ◽  
Induced Fit ◽  
Xylulose Kinase

scholarly journals Observing an Induced-fit Mechanism during Sequence-specific DNA Methylation

2006 ◽  
Vol 281 (48) ◽  
pp. 37205-37214 ◽  
Author(s):  
R. August Estabrook ◽  
Norbert Reich
Keyword(s):  
Dna Methylation ◽  
Induced Fit
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