scholarly journals Steered Molecular Dynamics of Lipid Membrane Indentation by Carbon and Silicon-Carbide Nanotubes—The Impact of Indenting Angle Uncertainty

Sensors ◽  
2021 ◽  
Vol 21 (21) ◽  
pp. 7011
Author(s):  
Przemysław Raczyński ◽  
Krzysztof Górny ◽  
Piotr Bełdowski ◽  
Steven Yuvan ◽  
Beata Marciniak ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Silicon Carbide ◽  
Molecular Dynamics Simulations ◽  
Lipid Membrane ◽  
Biological Membranes ◽  
Steered Molecular Dynamics ◽  
Phospholipid Membranes ◽  
Silicon Carbide Nanotubes ◽  
Dynamics Simulations ◽  
The Impact

Due to the semi-liquid nature and uneven morphologies of biological membranes, indentation may occur in a range of non-ideal conditions. These conditions are relatively unstudied and may alter the physical characteristics of the process. One of the basic challenges in the construction of nanoindenters is to appropriately align the nanotube tip and approach the membrane at a perpendicular angle. To investigate the impact of deviations from this ideal, we performed non-equilibrium steered molecular dynamics simulations of the indentation of phospholipid membranes by homogeneous CNT and non-homogeneous SiCNT indenters. We used various angles, rates, and modes of indentation, and the withdrawal of the relative indenter out of the membrane in corresponding conditions was simulated.

scholarly journals Separation of cyanide from an aqueous solution using armchair silicon carbide nanotubes: insights from molecular dynamics simulations

RSC Advances ◽  
2017 ◽  
Vol 7 (13) ◽  
pp. 7502-7508 ◽  
Author(s):  
Alireza Khataee ◽  
Golchehreh Bayat ◽  
Jafar Azamat
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Silicon Carbide ◽  
Molecular Dynamics Simulations ◽  
Silicon Carbide Nanotubes ◽  
Dynamics Simulations

Separation of cyanide, as a model contaminant, from aqueous solution was investigated using molecular dynamics simulations.

scholarly journals Molecular dynamics simulations of mechanical failure in polymorphic arrangements of amyloid fibrils containing structural defects

2013 ◽  
Vol 4 ◽  
pp. 429-440 ◽  
Author(s):  
Hlengisizwe Ndlovu ◽  
Alison E Ashcroft ◽  
Sheena E Radford ◽  
Sarah A Harris
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Steered Molecular Dynamics ◽  
Mechanical Failure ◽  
Structural Defects ◽  
Dynamics Simulations

We examine how the different steric packing arrangements found in amyloid fibril polymorphs can modulate their mechanical properties using steered molecular dynamics simulations. Our calculations demonstrate that for fibrils containing structural defects, their ability to resist force in a particular direction can be dominated by both the number and molecular details of the defects that are present. The simulations thereby suggest a hierarchy of factors that govern the mechanical resilience of fibrils, and illustrate the general principles that must be considered when quantifying the mechanical properties of amyloid fibres containing defects.

scholarly journals Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamic Networks ◽  
Aromatic Aldehydes ◽  
Active Site Residues ◽  
Trade Off ◽  
Highly Correlated ◽  
Dynamics Simulations ◽  
The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

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