Mechanisms of a Small Membrane-Active Antimicrobial Peptide from Hyla punctata

2020 ◽  
Vol 73 (3) ◽  
pp. 236 ◽  
Author(s):  
Charles H. Chen ◽  
Jakob P. Ulmschneider ◽  
Martin B. Ulmschneider
Keyword(s):  
Antimicrobial Peptide ◽  
Cell Model ◽  
Dynamic Structure ◽  
Md Simulations ◽  
Model Membranes ◽  
Membrane Thickness ◽  
Oligomeric Structure ◽  
The Past ◽  
Membrane Rigidity ◽  
Bacterial Model

Thousands of antimicrobial peptides have been observed and studied in the past decades; however, their membrane-active mechanisms are ambiguous due to their dynamic structure in the cell membrane. Here, we applied both molecular dynamics (MD) simulations and biophysical experiments to study the small membrane-active antimicrobial peptide Hylaseptin P1 (HSP1), which has significant selectivity towards anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG) and bacterial model membranes. HSP1 does not bind and fold onto human red blood cell model membranes, and it only binds, but does not fold, in zwitterionic 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) membranes. This suggests that the lipid chemistry and membrane rigidity are key to prevent HSP1 binding onto membranes, and the lipid headgroup charge may further promote peptide folding in the membrane. Our experiment-validated MD simulations suggest a carpet-like model mechanism for HSP1 through peptide binding, folding, aggregation, and assembly. HSP1 is shorter than the membrane thickness; therefore, the folded peptides aggregate on the surface, cross the membrane, and the oligomeric structure is supported by several surface-bound peptides in both bilayer leaflets.

scholarly journals Understanding Covalent Grafting of Nanotubes onto Polymer Nanocomposites: Molecular Dynamics Simulation Study

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2621
Author(s):  
Seunghwa Yang
Keyword(s):  
Molecular Dynamics ◽  
Load Transfer ◽  
Cell Model ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Covalent Grafting ◽  
Modelling Strategies ◽  
Multi Walled Carbon Nanotubes ◽  
Walled Carbon Nanotubes ◽  
External Loads

Here, we systematically interrogate the effects of grafting single-walled (SWNT) and multi-walled carbon nanotubes (MWNT) to polymer matrices by using molecular dynamics (MD) simulations. We specifically investigate key material properties that include interfacial load transfer, alteration of nanotube properties, and dispersion of nanotubes in the polymer matrix. Simulations are conducted on a periodic unit cell model of the nanocomposite with a straight carbon nanotube and an amorphous polyethylene terephthalate (PET) matrix. For each type of nanotube, either 0%, 1.55%, or 3.1% of the carbon atoms in the outermost nanotubes are covalently grafted onto the carbon atoms of the PET matrix. Stress-strain curves and the elastic moduli of nanotubes and nanocomposites are determined based on the density of covalent grafting. Covalent grafting promotes two rivalling effects with respect to altering nanotube properties, and improvements in interfacial load transfer in the nanocomposites are clearly observed. The enhanced interface enables external loads applied to the nanocomposites to be efficiently transferred to the grafted nanotubes. Covalent functionalization of the nanotube surface with PET molecules can alter the solubility of nanotubes and improve dispersibility. Finally, we discuss the current limitations and challenges in using molecular modelling strategies to accurately predict properties on the nanotube and polymers systems studied here.

scholarly journals Retrotransposon-induced mosaicism in the neural genome

Open Biology ◽  
2018 ◽  
Vol 8 (7) ◽  
pp. 180074 ◽  
Author(s):  
Gabriela O. Bodea ◽  
Eleanor G. Z. McKelvey ◽  
Geoffrey J. Faulkner
Keyword(s):  
Brain Development ◽  
Adult Neurogenesis ◽  
Neurological Disease ◽  
Dynamic Structure ◽  
Neurological Function ◽  
Developing Brain ◽  
Neural Cells ◽  
The Past ◽  
Retrotransposon Activity ◽  
The Brain

Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.

Molecular Dynamic Structure Investigations of the Surface Stability and Adsorption of H, H2, CH3, C2H2: (100) Diamond

1992 ◽  
Vol 270 ◽  
Author(s):  
Th. Frauenheim ◽  
P. Blaudeck ◽  
D. Porezag
Keyword(s):  
Density Functional ◽  
Dynamic Structure ◽  
Md Simulations ◽  
Diamond Surface ◽  
Diamond Growth ◽  
Minimal Basis ◽  
Surface Stability ◽  
Hydrogen Supply ◽  
Reaction Processes ◽  
Structure Investigations

ABSTRACTSurface properties - stability and reconstruction - of clean and hydrogenated diamond (100) have been studied by real temperature molecular dynarnic (MD) simulations using an approximate density functional (DF) theory expanding the total electronic wave function in a minimal basis of localized atomic valence electron orbitals (LCAO - ansatz). The clean surface is highly unstable against a spontaneous dimerization resulting in a 2×1 reconstruction. Atomic hydrogen in the gas phase above the top surface at all temperatures and H2 molecules approaching the center of the dimer bond at room temperature are reactive in breaking the dimer π-bonds forming a monohydrogenated surface which maintains a stable 2×1 structure but with elongated surface C-C dimer bonds remaining stable against continuing hydrogen supply. The dihydrogenated surface taking a 1×1 structure, because of steric overcrowding dynamically becomes unstable against forming a 1×1 (alternating) di-, monohydrogenated surface. As first elementary reaction processes which may be discussed in relation to diamond growth we studied the thermal adsorption of CH3 and C2H2 onto a clean 2×l reconstructed (100) diamond surface.

Bacterial Model Membranes Reshape Fibrillation of a Functional Amyloid Protein

Biochemistry ◽  
2018 ◽  
Vol 57 (35) ◽  
pp. 5230-5238 ◽  
Author(s):  
Ravit Malishev ◽  
Razan Abbasi ◽  
Raz Jelinek ◽  
Liraz Chai
Keyword(s):  
Model Membranes ◽  
Amyloid Protein ◽  
Functional Amyloid ◽  
Bacterial Model

scholarly journals Dewetting-Induced Formation of Bacterial Model Membranes using Submicron Shell Double Emulsions

2019 ◽  
Vol 116 (3) ◽  
pp. 226a
Author(s):  
Sepehr Maktabi ◽  
Noah Malmstadt ◽  
Jeffrey Schertzer ◽  
Paul Chiarot
Keyword(s):  
Model Membranes ◽  
Double Emulsions ◽  
Bacterial Model
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