scholarly journals Full elucidation of the transmembrane anion transport mechanism of squaramides using in silico investigations

2018 ◽  
Vol 20 (32) ◽  
pp. 20796-20811 ◽  
Author(s):  
Igor Marques ◽  
Pedro M. R. Costa ◽  
Margarida Q. Miranda ◽  
Nathalie Busschaert ◽  
Ethan N. W. Howe ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Transport Mechanism ◽  
Anion Transport ◽  
Carrier Mechanism ◽  
Anion Carrier

The anion carrier mechanism promoted by squaramide-based molecules has been elucidated by molecular dynamics and chloride efflux studies.

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 Proton Transport Mechanism and Pathways in the Superprotonic Phase of M3H(AO4)2 Solid Acids from Ab Initio Molecular Dynamics Simulations

2021 ◽  
Author(s):  
Boris Merinov ◽  
Sergey Morozov
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Proton Transport ◽  
Transport Mechanism ◽  
Solid Acids ◽  
Ab Initio Molecular Dynamics ◽  
Theoretical Studies ◽  
Dynamics Simulations ◽  
Experimental And Theoretical Studies ◽  
Superprotonic Phase

The proton transport mechanism in superprotonic phases of solid acids is a subject of experimental and theoretical studies for a number of years. Despite this, details of the mechanism still...

In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach

2021 ◽  
Vol 27 (2) ◽  
Author(s):  
Marzieh Gharouni ◽  
Hamid Mosaddeghi ◽  
Jamshid Mehrzad ◽  
Ali Es-haghi ◽  
Alireza Motavalizadehkakhky
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Metal Ion ◽  
Methyl Transferase ◽  
Zinc Metal ◽  
Structural Insights

In silico profiling and structural insights of missense mutations in RET protein kinase domain by molecular dynamics and docking approach

2014 ◽  
Vol 10 (3) ◽  
pp. 421-436 ◽  
Author(s):  
C. George Priya Doss ◽  
B. Rajith ◽  
Chiranjib Chakraboty ◽  
V. Balaji ◽  
R. Magesh ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Protein Kinase ◽  
In Silico ◽  
Kinase Domain ◽  
Missense Mutations ◽  
Protein Kinase Domain ◽  
Docking Approach ◽  
Structural Insights

scholarly journals Exploring the pH-Dependent Substrate Transport Mechanism of FocA Using Molecular Dynamics Simulation

2013 ◽  
Vol 105 (12) ◽  
pp. 2714-2723 ◽  
Author(s):  
Xiaoying Lv ◽  
Huihui Liu ◽  
Meng Ke ◽  
Haipeng Gong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Transport Mechanism ◽  
Dynamics Simulation ◽  
Substrate Transport ◽  
Ph Dependent

In Silico Targeting Human Multidrug Transporter ABCG2 in Breast Cancer: Database Screening, Molecular Docking, and Molecular Dynamics Study

2021 ◽  
pp. 2060039
Author(s):  
Mahmoud A. A. Ibrahim ◽  
Esraa A. A. Badr ◽  
Alaa H. M. Abdelrahman ◽  
Nahlah Makki Almansour ◽  
Gamal A. H. Mekhemer ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Molecular Dynamics ◽  
Molecular Docking ◽  
In Silico ◽  
Multidrug Transporter ◽  
Database Screening
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