EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations

2021 ◽  
Vol 17 (2) ◽  
pp. 1181-1193
Author(s):  
Semen Yesylevskyy ◽  
Himanshu Khandelia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Simple Technique ◽  
Membrane Curvature ◽  
Dynamics Simulations

scholarly journals Chiral twisting in cytoskeletal polymers regulates filament size and orientation

2018 ◽  
Author(s):  
Handuo Shi ◽  
David Quint ◽  
Ajay Gopinathan ◽  
Kerwyn Casey Huang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Caulobacter Crescentus ◽  
Membrane Binding ◽  
Membrane Curvature ◽  
Cytoskeletal Proteins ◽  
Coarse Grained ◽  
Biophysical Model ◽  
Dynamics Simulations

AbstractWhile cytoskeletal proteins in the actin family are structurally similar, as filaments they act as critical components of diverse cellular processes across all kingdoms of life. In many rod-shaped bacteria, the actin homolog MreB directs cell-wall insertion and maintains cell shape, but it remains unclear how structural changes to MreB affect its physiological function. To bridge this gap, we performed molecular dynamics simulations forCaulobacter crescentusMreB and then utilized a coarse-grained biophysical model to successfully predict MreB filament propertiesin vivo.We discovered that MreB double protofilaments exhibit left-handed twisting that is dependent on the bound nucleotide and membrane binding; the degree of twisting determines the limit length and orientation of MreB filamentsin vivo.Membrane binding of MreB also induces a stable membrane curvature that is physiologically relevant. Together, our data empower the prediction of cytoskeletal filament size from molecular dynamics simulations, providing a paradigm for connecting protein filament structure and mechanics to cellular functions.

scholarly journals Curvature induction and sensing of the F-BAR protein Pacsin1 on lipid membranes via molecular dynamics simulations

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Md. Iqbal Mahmood ◽  
Hiroshi Noguchi ◽  
Kei-ichi Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Lipid Membranes ◽  
Lipid Membrane ◽  
Complex Structure ◽  
Membrane Curvature ◽  
Coarse Grained ◽  
Lateral Interaction ◽  
Bar Domain ◽  
Dynamics Simulations

Abstract F-Bin/Amphiphysin/Rvs (F-BAR) domain proteins play essential roles in biological processes that involve membrane remodelling, such as endocytosis and exocytosis. It has been shown that such proteins transform the lipid membrane into tubes. Notably, Pacsin1 from the Pacsin/Syndapin subfamily has the ability to transform the membrane into various morphologies: striated tubes, featureless wide and thin tubes, and pearling vesicles. The molecular mechanism of this interesting ability remains elusive. In this study, we performed all-atom (AA) and coarse-grained (CG) molecular dynamics simulations to investigate the curvature induction and sensing mechanisms of Pacsin1 on a membrane. From AA simulations, we show that Pacsin1 has internal structural flexibility. In CG simulations with parameters tuned from the AA simulations, spontaneous assembly of two Pacsin1 dimers through lateral interaction is observed. Based on the complex structure, we show that the regularly assembled Pacsin1 dimers bend a tensionless membrane. We also show that a single Pacsin1 dimer senses the membrane curvature, binding to a buckled membrane with a preferred curvature. These results provide molecular insights into polymorphic membrane remodelling.

scholarly journals Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

2019 ◽  
Author(s):  
Semen Yesylevskyy ◽  
Timothée Rivel ◽  
Christophe Ramseyer
Keyword(s):  
Molecular Dynamics ◽  
Plasma Membrane ◽  
Molecular Dynamics Simulations ◽  
Membrane Curvature ◽  
Cancer Drugs ◽  
Anti Cancer ◽  
Membrane Bending ◽  
Dynamics Simulations

ABSTRACTIn this work the permeability of a model asymmetric plasma membrane, for ions, water and the anti-cancer drugs cisplatin and gemcitabine is studied by means of all-atom molecular dynamics simulations. It is shown that permeability of the membranes increases from one to three orders of magnitude upon membrane bending depending on the compound and the sign of curvature. Our results show that the membrane curvature is an important factor which should be considered during evaluation of drug translocation.TOC GRAPHICS

scholarly journals Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Semen Yesylevskyy ◽  
Timothée Rivel ◽  
Christophe Ramseyer
Keyword(s):  
Molecular Dynamics ◽  
Plasma Membrane ◽  
Molecular Dynamics Simulations ◽  
Membrane Curvature ◽  
Cancer Drugs ◽  
Anti Cancer ◽  
Membrane Bending ◽  
Dynamics Simulations ◽  
Curved Membrane ◽  
First Time

AbstractIn this work the permeability of a model asymmetric plasma membrane, for ions, water and the anti-cancer drugs cisplatin and gemcitabine is studied by means of all-atom molecular dynamics simulations. It is shown for the first time that permeability of the highly curved membrane increases from one to three orders of magnitude upon membrane bending depending on the compound and the sign of curvature. Our results suggest that the membrane curvature could be an important factor of drug translocation through the membrane.

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