Molecular Dynamics Study of the Behavior of Selected Nanoscale Building Blocks in a Gel-Phase Lipid Bilayer

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

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Dynamic regulation of HIV-1 capsid interaction with the restriction factor TRIM5α identified by magic-angle spinning NMR and molecular dynamics simulations

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1800796115 ◽

2018 ◽

Vol 115 (45) ◽

pp. 11519-11524 ◽

Cited By ~ 22

Author(s):

Caitlin M. Quinn ◽

Mingzhang Wang ◽

Matthew P. Fritz ◽

Brent Runge ◽

Jinwoo Ahn ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Building Blocks ◽

Magic Angle Spinning ◽

Magic Angle ◽

Capsid Assembly ◽

Dynamic Regulation ◽

Angle Spinning ◽

Dynamics Simulations ◽

Hiv 1

The host factor protein TRIM5α plays an important role in restricting the host range of HIV-1, interfering with the integrity of the HIV-1 capsid. TRIM5 triggers an antiviral innate immune response by functioning as a capsid pattern recognition receptor, although the precise mechanism by which the restriction is imposed is not completely understood. Here we used an integrated magic-angle spinning nuclear magnetic resonance and molecular dynamics simulations approach to characterize, at atomic resolution, the dynamics of the capsid’s hexameric and pentameric building blocks, and the interactions with TRIM5α in the assembled capsid. Our data indicate that assemblies in the presence of the pentameric subunits are more rigid on the microsecond to millisecond timescales than tubes containing only hexamers. This feature may be of key importance for controlling the capsid’s morphology and stability. In addition, we found that TRIM5α binding to capsid induces global rigidification and perturbs key intermolecular interfaces essential for higher-order capsid assembly, with structural and dynamic changes occurring throughout the entire CA polypeptide chain in the assembly, rather than being limited to a specific protein-protein interface. Taken together, our results suggest that TRIM5α uses several mechanisms to destabilize the capsid lattice, ultimately inducing its disassembly. Our findings add to a growing body of work indicating that dynamic allostery plays a pivotal role in capsid assembly and HIV-1 infectivity.

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A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA

RSC Advances ◽

10.1039/c5ra10965e ◽

2015 ◽

Vol 5 (83) ◽

pp. 68227-68233 ◽

Cited By ~ 9

Author(s):

Jipeng Li ◽

Yiyun Ouyang ◽

Xian Kong ◽

Jingying Zhu ◽

Diannan Lu ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Lipid Bilayer ◽

Dynamics Simulation ◽

Lipid Bilayer Membranes ◽

Bilayer Membranes ◽

Multi Scale

PMAL as a novel carrier for the delivery of siRNA into lipid bilayer membranes.

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Variation of thermal conductivity of DPPC lipid bilayer membranes around the phase transition temperature

Journal of The Royal Society Interface ◽

10.1098/rsif.2017.0127 ◽

2017 ◽

Vol 14 (130) ◽

pp. 20170127 ◽

Cited By ~ 11

Author(s):

Sina Youssefian ◽

Nima Rahbar ◽

Christopher R. Lambert ◽

Steven Van Dessel

Keyword(s):

Phase Transition ◽

Thermal Conductivity ◽

Thermal Properties ◽

Transition Temperature ◽

Lipid Bilayer ◽

Lipid Bilayers ◽

Phase Transition Temperature ◽

Temperature Gradients ◽

Phase Behaviour ◽

Gel Phase

Given their amphiphilic nature and chemical structure, phospholipids exhibit a strong thermotropic and lyotropic phase behaviour in an aqueous environment. Around the phase transition temperature, phospholipids transform from a gel-like state to a fluid crystalline structure. In this transition, many key characteristics of the lipid bilayers such as structure and thermal properties alter. In this study, we employed atomistic simulation techniques to study the structure and underlying mechanisms of heat transfer in dipalmitoylphosphatidylcholine (DPPC) lipid bilayers around the fluid–gel phase transformation. To investigate this phenomenon, we performed non-equilibrium molecular dynamics simulations for a range of different temperature gradients. The results show that the thermal properties of the DPPC bilayer are highly dependent on the temperature gradient. Higher temperature gradients cause an increase in the thermal conductivity of the DPPC lipid bilayer. We also found that the thermal conductivity of DPPC is lowest at the transition temperature whereby one lipid leaflet is in the gel phase and the other is in the liquid crystalline phase. This is essentially related to a growth in thermal resistance between the two leaflets of lipid at the transition temperature. These results provide significant new insights into developing new thermal insulation for engineering applications.

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