scholarly journals Ion-dependent structure, dynamics, and allosteric coupling in a non-selective cation channel

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Adam Lewis ◽  
Vilius Kurauskas ◽  
Marco Tonelli ◽  
Katherine Henzler-Wildman
Keyword(s):  
Bound States ◽  
Direct Evidence ◽  
Md Simulations ◽  
Structural Heterogeneity ◽  
Cation Channel ◽  
Solution Nmr ◽  
Allosteric Coupling ◽  
Structure And Dynamics ◽  
Multiple Conformations ◽  
Pore Lining

AbstractThe selectivity filter (SF) determines which ions are efficiently conducted through ion channel pores. NaK is a non-selective cation channel that conducts Na+ and K+ with equal efficiency. Crystal structures of NaK suggested a rigid SF structure, but later solid-state NMR and MD simulations questioned this interpretation. Here, we use solution NMR to characterize how bound Na+ vs. K+ affects NaK SF structure and dynamics. We find that the extracellular end of the SF is flexible on the ps-ns timescale regardless of bound ion. On a slower timescale, we observe a structural change between the Na+ and K+-bound states, accompanied by increased structural heterogeneity in Na+. We also show direct evidence that the SF structure is communicated to the pore via I88 on the M2 helix. These results support a dynamic SF with multiple conformations involved in non-selective conduction. Our data also demonstrate allosteric coupling between the SF and pore-lining helices in a non-selective cation channel that is analogous to the allosteric coupling previously demonstrated for K+-selective channels, supporting the generality of this model.

scholarly journals Ion-dependent structure, dynamics, and allosteric coupling in a non-selective cation channel

2021 ◽  
Author(s):  
Adam Lewis ◽  
Vilius Kurauskas ◽  
Marco Tonelli ◽  
Katherine Henzler-Wildman
Keyword(s):  
Bound States ◽  
Direct Evidence ◽  
Md Simulations ◽  
Structural Heterogeneity ◽  
Cation Channel ◽  
Solution Nmr ◽  
Allosteric Coupling ◽  
Structure And Dynamics ◽  
Multiple Conformations ◽  
Pore Lining

The selectivity filter (SF) determines which ions are efficiently conducted through ion channel pores. NaK is a non-selective cation channel that conducts Na+ and K+ with equal efficiency. Crystal structures of NaK suggested a rigid SF structure, but later solid-state NMR and MD simulations questioned this interpretation. Here, we use solution NMR to characterize how bound Na+ vs. K+ affects NaK SF structure and dynamics. We find that the extracellular end of the SF is flexible on the ps-ns timescale regardless of bound ion. On a slower timescale, we observe a structural change between the Na+ and K+-bound states, accompanied by increased structural heterogeneity in Na+. We also show direct evidence that the SF structure is communicated to the pore via I88 on the M2 helix. These results support a dynamic SF with multiple conformations involved in non-selective conduction. Our data also demonstrate allosteric coupling between the SF and pore-lining helices in a non-selective cation channel that is analogous to the allosteric coupling previously demonstrated for K+-selective channels, supporting the generality of this model.

Solution structure and dynamics of S100A5 in the apo and Ca2+-bound states

2009 ◽  
Vol 14 (7) ◽  
pp. 1097-1107 ◽  
Author(s):  
Ivano Bertini ◽  
Soumyasri Das Gupta ◽  
Xiaoyu Hu ◽  
Tilemachos Karavelas ◽  
Claudio Luchinat ◽  
...  
Keyword(s):  
Bound States ◽  
Solution Structure ◽  
Structure And Dynamics

scholarly journals Sorption, Structure and Dynamics of CO2 and Ethane in Silicalite at High Pressure: A Combined Monte Carlo and Molecular Dynamics Simulation Study

Molecules ◽  
2018 ◽  
Vol 24 (1) ◽  
pp. 99 ◽  
Author(s):  
Siddharth Gautam ◽  
Tingting Liu ◽  
David Cole
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Time Scales ◽  
Rotational Motion ◽  
High Pressures ◽  
Sorption Isotherms ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Structure And Dynamics ◽  
Low Pressures

Silicalite is an important nanoporous material that finds applications in several industries, including gas separation and catalysis. While the sorption, structure, and dynamics of several molecules confined in the pores of silicalite have been reported, most of these studies have been restricted to low pressures. Here we report a comparative study of sorption, structure, and dynamics of CO2 and ethane in silicalite at high pressures (up to 100 bar) using a combination of Monte Carlo (MC) and molecular dynamics (MD) simulations. The behavior of the two fluids is studied in terms of the simulated sorption isotherms, the positional and orientational distribution of sorbed molecules in silicalite, and their translational diffusion, vibrational spectra, and rotational motion. Both CO2 and ethane are found to exhibit orientational ordering in silicalite pores; however, at high pressures, while CO2 prefers to reside in the channel intersections, ethane molecules reside mostly in the sinusoidal channels. While CO2 exhibits a higher self-diffusion coefficient than ethane at low pressures, at high pressures, it becomes slower than ethane. Both CO2 and ethane exhibit rotational motion at two time scales. At both time scales, the rotational motion of ethane is faster. The differences observed here in the behavior of CO2 and ethane in silicalite pores can be seen as a consequence of an interplay of the kinetic diameter of the two molecules and the quadrupole moment of CO2.

scholarly journals Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Ronak Y. Patel ◽  
Petety V. Balaji
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayers ◽  
Membrane Structure ◽  
Lipid Membrane ◽  
Biological Membranes ◽  
Md Simulations ◽  
Atomic Level ◽  
Structure And Dynamics ◽  
Hydrogen Bonding Interactions ◽  
Dynamics Simulations

Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.

scholarly journals Dynamic Protein-Protein Complexes: How Alternative Interactions Create Ensembles and How Solution NMR and MD Simulations can Characterize them

2012 ◽  
Vol 102 (3) ◽  
pp. 608a-609a
Author(s):  
Matthias Buck ◽  
Liqun Zhang ◽  
Hyeong J. Lee ◽  
Prasanta K. Hota
Keyword(s):  
Protein Complexes ◽  
Md Simulations ◽  
Solution Nmr

scholarly journals Structure and Dynamics of K Channel Pore-Lining Helices: A Comparative Simulation Study

2000 ◽  
Vol 78 (1) ◽  
pp. 79-92 ◽  
Author(s):  
Indira H. Shrivastava ◽  
Charlotte E. Capener ◽  
Lucy R. Forrest ◽  
Mark S.P. Sansom
Keyword(s):  
Simulation Study ◽  
K Channel ◽  
Channel Pore ◽  
Structure And Dynamics ◽  
Pore Lining
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