scholarly journals Molecular dynamics simulations of a DNA photolyase protein: High-mobility and conformational changes of the FAD molecule at low temperatures

2012 ◽  
Vol 03 (03) ◽  
pp. 169-180 ◽  
Author(s):  
Kholmirzo Kholmurodov ◽  
Ermuhammad Dushanov ◽  
Kenji Yasuoka
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Low Temperatures ◽  
High Mobility ◽  
Dna Photolyase ◽  
Dynamics Simulations

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

scholarly journals Local Structuring of Diketopyrrolopyrrole (DPP)-based Oligomers from Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Maryam Reisjalali ◽  
J. Javier Burgos-Marmol ◽  
Rex Manurung ◽  
Alessandro Troisi
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Mobility ◽  
Semiconducting Polymers ◽  
Microscopic Structure ◽  
Dynamics Simulations

The microscopic structure of high mobility semiconducting polymers is known to be essential for their performance but it cannot be easily deduced from the available experimental data. A series of...

scholarly journals A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0121092 ◽  
Author(s):  
Brian J. Bennion ◽  
Sebnem G. Essiz ◽  
Edmond Y. Lau ◽  
Jean-Luc Fattebert ◽  
Aiyana Emigh ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Dynamics Simulations

scholarly journals Molecular Dynamics Simulations for Conformational Changes on a Reaction Step of SR-Ca2+-ATPase

2018 ◽  
Vol 114 (3) ◽  
pp. 341a
Author(s):  
Chigusa Kobayashi ◽  
Yasuhiro Matsunaga ◽  
Jaewoon Jung ◽  
Yuji Sugita
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Reaction Step ◽  
Dynamics Simulations
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