Conformational Dynamics and Protein–Substrate Interaction of ABC Transporter BtuCD at the Occluded State Revealed by Molecular Dynamics Simulations

Biochemistry ◽  
2016 ◽  
Vol 55 (49) ◽  
pp. 6897-6907 ◽  
Author(s):  
Chao Pan ◽  
Jingwei Weng ◽  
Wenning Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Abc Transporter ◽  
Conformational Dynamics ◽  
Protein Substrate ◽  
Substrate Interaction ◽  
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 Molecular dynamics simulations reveal distinct differences in conformational dynamics and thermodynamics between the unliganded and CD4-bound states of HIV-1 gp120

2020 ◽  
Vol 22 (10) ◽  
pp. 5548-5560
Author(s):  
Yi Li ◽  
Lei Deng ◽  
Jing Liang ◽  
Guang-Heng Dong ◽  
Yuan-Ling Xia ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Bound States ◽  
Conformational Dynamics ◽  
Immunological Properties ◽  
Dynamics Simulations ◽  
Hiv Gp120 ◽  
Hiv 1

Large changes in dynamics and thermodynamics of gp120 upon CD4 binding account for the functional and immunological properties of HIV/gp120.

scholarly journals Conformational dynamics of a crystalline protein from microsecond-scale molecular dynamics simulations and diffuse X-ray scattering

2014 ◽  
Vol 111 (50) ◽  
pp. 17887-17892 ◽  
Author(s):  
Michael E. Wall ◽  
Andrew H. Van Benschoten ◽  
Nicholas K. Sauter ◽  
Paul D. Adams ◽  
James S. Fraser ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Dynamics ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering

scholarly journals Insights into the anthrax lethal factor-substrate interaction and selectivity using docking and molecular dynamics simulations

2009 ◽  
Vol 18 (8) ◽  
pp. 1774-1785 ◽  
Author(s):  
Georgios A. Dalkas ◽  
Athanasios Papakyriakou ◽  
Alexios Vlamis-Gardikas ◽  
Georgios A. Spyroulias
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lethal Factor ◽  
Substrate Interaction ◽  
Anthrax Lethal Factor ◽  
Dynamics Simulations

A study on the structural features of SELK, an over-expressed protein in hepatocellular carcinoma, by molecular dynamics simulations in a lipid–water system

2016 ◽  
Vol 12 (10) ◽  
pp. 3209-3222 ◽  
Author(s):  
Andrea Polo ◽  
Stefano Guariniello ◽  
Giovanni Colonna ◽  
Gennaro Ciliberto ◽  
Susan Costantini
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Dynamics ◽  
Water System ◽  
Structural Features ◽  
System P ◽  
Dynamics Simulations

Terminal regions in SELK present different conformational dynamics being coupled complicatedly through the membrane.

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