scholarly journals Can polarity-inverted membranes self-assemble on Titan?

2020 ◽  
Vol 6 (4) ◽  
pp. eaax0272 ◽  
Author(s):  
H. Sandström ◽  
M. Rahm
Keyword(s):  
Molecular Dynamics ◽  
Low Temperature ◽  
Lipid Bilayers ◽  
Self Assembly ◽  
Liquid Hydrocarbon ◽  
Bilayer Membrane ◽  
Cryogenic Liquid ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Dynamics Simulations

The environmental and chemical limits of life are two of the most central questions in astrobiology. Our understanding of life’s boundaries has implications on the efficacy of biosignature identification in exoplanet atmospheres and in the solar system. The lipid bilayer membrane is one of the central prerequisites for life as we know it. Previous studies based on molecular dynamics simulations have suggested that polarity-inverted membranes, azotosomes, made up of small nitrogen-containing molecules, are kinetically persistent and may function on cryogenic liquid hydrocarbon worlds, such as Saturn’s moon Titan. We here take the next step and evaluate the thermodynamic viability of azotosome formation. Quantum mechanical calculations predict that azotosomes are not viable candidates for self-assembly akin to lipid bilayers in liquid water. We argue that cell membranes may be unnecessary for hypothetical astrobiology under stringent anhydrous and low-temperature conditions akin to those of Titan.

scholarly journals Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study

2015 ◽  
Vol 11 (4) ◽  
pp. 1041-1051 ◽  
Author(s):  
Tanya Singh ◽  
Olayiwola Adedotun Adekoya ◽  
B. Jayaram
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Matrix Metalloproteinases ◽  
Matrix Metalloproteinase ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Important Class ◽  
Matrix Metalloproteinase Inhibitors ◽  
Metalloproteinase Inhibitors ◽  
Dynamics Simulations

A computationally tractable pathway which helped in understanding the binding of matrix metalloproteinase inhibitors against an important class of MMPs is presented in this article.

scholarly journals A molecular dynamics simulation study on the propensity of Asn-Gly-containing heptapeptides towards β-turn structures: Comparison with ab initio quantum mechanical calculations

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243429
Author(s):  
Dimitrios A. Mitsikas ◽  
Nicholas M. Glykos
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Type I ◽  
Quantum Mechanical Calculations ◽  
Water Solvent ◽  
Simulation Protocol ◽  
Dynamics Simulations

Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 μs each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations within the DFT framework have shown that these peptides adopt β-turn structures in aqueous solution, with type I’ β-turn being the most preferred motif. The results from our analyses indicate that at least for the given systems, force field and simulation protocol, the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.

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