Molecular Dynamics Simulations of Membranes Composed of Glycolipids and Phospholipids

Kapla, Jon; Stevensson, Baltzar; Dahlberg, Martin; Maliniak, Arnold

doi:10.1021/jp209268p

Cited by 30 publications

(33 citation statements)

References 84 publications

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“…Thus, the DOPC PN vector is, on average, almost parallel to the bilayer surface, whereas the DOPC CN and MGDG CO and CC vectors are tilted ~ 60° relative to the bilayer surface. The value of the preferred orientation of the PN vector as well as a broad distribution of the ω angle agree well with experimental data in Refs and other MD simulations . The values of the preferred orientation of the MGDG head group vectors are in accord with NMR spectroscopy data of Howard and Prestegard showing that galactose head group of MGDG is tilted to the bilayer surface and also with values obtained in other computational studies, of ~ 40° for the CO vector and ~ 30° for the CC vector .…”

Section: Resultssupporting

confidence: 89%

Is the tilt of the lipid head group correlated with the number of intermolecular interactions at the bilayer interface?

2018

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Lipid and water molecules comprising the bilayer form an integral entity owing to only weak physical interactions. At the bilayer interface, these interactions chiefly involve hydrogen bonding and charge pairing. Lipid head groups make hydrogen bonds (H-bonds) predominantly with water, whereas interlipid H-bonds and charge pairs are less numerous. Both interlipid H-bonding and charge pairing depend on the distance and relative orientation of the interacting head groups. In this computational paper, correlations are analysed between the orientation of the lipid head group and the number of interlipid interactions at the interface of a bilayer made of galactolipids, forming direct interlipid H-bonds, and of phosphatidylcholines forming interlipid charge pairs. The correlations are not strong, however, in both bilayers they show a similar trend.

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Section: Resultssupporting

confidence: 89%

Is the tilt of the lipid head group correlated with the number of intermolecular interactions at the bilayer interface?

2018

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“… 28 − 37 The general conclusion from these studies seems to be that the CHARMM-based, 29 , 31 GAFFlipid, 33 and MacRog 37 force fields performs better for the glycerol backbone and headgroup structures than the GROMOS-based models. 30 , 32 , 34 , 35 However, none of the studies exploits the full potential of the available experimental data discussed in the previous section, i.e. the quantitative accuracy, known signs, and stereospecific labeling of the experimental order parameters.…”

Section: Resultsmentioning

confidence: 99%

Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions

et al. 2015

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Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR experiments in terms of the highly structurally sensitive C–H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P–N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files () has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.

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“…We determine the orientations of the local-mode ls based on the transition charges in the amide plane 66,67 and the orientations and magnitudes of the as based on previous work of Tsuboi et al 68 The orientation distribution of the ester groups in the MGDG/PG lipid monolayer layer was determined from a published MD trajectory 69 .…”

Section: Methodsmentioning

confidence: 99%

IM30 triggers membrane fusion in cyanobacteria and chloroplasts

et al. 2015

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The thylakoid membrane of chloroplasts and cyanobacteria is a unique internal membrane system harbouring the complexes of the photosynthetic electron transfer chain. Despite their apparent importance, little is known about the biogenesis and maintenance of thylakoid membranes. Although membrane fusion events are essential for the formation of thylakoid membranes, proteins involved in membrane fusion have yet to be identified in photosynthetic cells or organelles. Here we show that IM30, a conserved chloroplast and cyanobacterial protein of approximately 30 kDa binds as an oligomeric ring in a well-defined geometry specifically to membranes containing anionic lipids. Triggered by Mg 2 þ , membrane binding causes destabilization and eventually results in membrane fusion. We propose that IM30 establishes contacts between internal membrane sites and promotes fusion to enable regulated exchange of proteins and/or lipids in cyanobacteria and chloroplasts.

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Molecular Dynamics Simulations of Membranes Composed of Glycolipids and Phospholipids

Cited by 30 publications

References 84 publications

Is the tilt of the lipid head group correlated with the number of intermolecular interactions at the bilayer interface?

Is the tilt of the lipid head group correlated with the number of intermolecular interactions at the bilayer interface?

Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions

IM30 triggers membrane fusion in cyanobacteria and chloroplasts

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