Atomistic detailed free‐energy landscape of intrinsically disordered protein studied by multi‐scale divide‐and‐conquer molecular dynamics simulation

2020 ◽  
Vol 42 (1) ◽  
pp. 19-26
Author(s):  
Hiromitsu Shimoyama ◽  
Yasushige Yonezawa
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Energy Landscape ◽  
Intrinsically Disordered Protein ◽  
Divide And Conquer ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Multi Scale ◽  
Intrinsically Disordered ◽  
Disordered Protein

scholarly journals A Free-Energy Landscape Analysis of Calmodulin Obtained from an NMR Data-Utilized Multi-Scale Divide-and-Conquer Molecular Dynamics Simulation

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1241
Author(s):  
Hiromitsu Shimoyama ◽  
Yasuteru Shigeta
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Structural Change ◽  
Conformational Changes ◽  
Calcium Binding ◽  
Structural Changes ◽  
Energy Landscape ◽  
Divide And Conquer ◽  
Free Energy Landscape ◽  
Multi Scale

Calmodulin (CaM) is a multifunctional calcium-binding protein, which regulates a variety of biochemical processes. CaM acts through its conformational changes and complex formation with its target enzymes. CaM consists of two globular domains (N-lobe and C-lobe) linked by an extended linker region. Upon calcium binding, the N-lobe and C-lobe undergo local conformational changes, followed by a major conformational change of the entire CaM to wrap the target enzyme. However, the regulation mechanisms, such as allosteric interactions, which regulate the large structural changes, are still unclear. In order to investigate the series of structural changes, the free-energy landscape of CaM was obtained by multi-scale divide-and-conquer molecular dynamics (MSDC-MD). The resultant free-energy landscape (FEL) shows that the Ca2+ bound CaM (holo-CaM) would take an experimentally famous elongated structure, which can be formed in the early stage of structural change, by breaking the inter-domain interactions. The FEL also shows that important interactions complete the structural change from the elongated structure to the ring-like structure. In addition, the FEL might give a guiding principle to predict mutational sites in CaM. In this study, it was demonstrated that the movement process of macroscopic variables on the FEL may be diffusive to some extent, and then, the MSDC-MD is suitable to the parallel computation.

The regulation mechanism of phosphorylation and mutations in intrinsically disordered protein 4E-BP2

2020 ◽  
Vol 22 (5) ◽  
pp. 2938-2948
Author(s):  
Ke Wang ◽  
Shangbo Ning ◽  
Yue Guo ◽  
Mojie Duan ◽  
Minghui Yang
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Intrinsically Disordered Protein ◽  
Regulation Mechanism ◽  
Energy Landscapes ◽  
Intrinsically Disordered ◽  
Disordered Protein ◽  
Free Energy Landscapes

The free energy landscapes of 4E-BP2 and its variants were obtained by replica-exchanged molecular dynamics, which elucidate the regulation mechanism of phosphorylation and mutations on the intrinsically disordered protein.

scholarly journals Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation

2007 ◽  
Vol 3 ◽  
pp. 757-766
Author(s):  
Masakazu Sekijima ◽  
Jun Doi ◽  
Shinya Honda ◽  
Tamotsu Noguchi ◽  
Shigenori Shimizu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Parallel Molecular Dynamics ◽  
Analysis System

scholarly journals Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms

RSC Advances ◽  
2017 ◽  
Vol 7 (46) ◽  
pp. 28580-28590 ◽  
Author(s):  
Peng Sang ◽  
Xing Du ◽  
Li-Quan Yang ◽  
Zhao-Hui Meng ◽  
Shu-Qun Liu
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Cold Adaptation ◽  
Energy Landscape ◽  
Serine Proteinase ◽  
Dynamics Simulation ◽  
Proteinase K ◽  
Free Energy Landscape ◽  
Molecular Motions ◽  
Underlying Mechanisms

The physicochemical bases for enzyme cold-adaptation remain elusive.

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