Headgroup Mediated Water Insertion into the DPPC Bilayer: A Molecular Dynamics Study

Pandey, Prithvi Raj; Roy, Sudip

doi:10.1021/jp1090203

Cited by 36 publications

(33 citation statements)

References 52 publications

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“…During the NPT simulation run (constant number of particles, constant pressure and constant temperature) we monitored the surface area per lipid considering the total surface along the XY plane (plane parallel to the bilayer surface) divided by the number of lipids in one lamellar layer. 24 The final area per lipid was 60.5 Å 2 (see the top panel of Fig. 3), which is consistent with the expected result of CHARMM36 force field (60.8 Å 2 ) 18 and also with the experimental value (60.6 Å 2 ).…”

Section: Computational Detailssupporting

confidence: 88%

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

Yang

Calero

Martı́

2014

The Journal of Chemical Physics

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Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10 −5 cm 2 /s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10 −8 cm 2 /s). In the intermediate regime of subdiffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2-8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a "wagging of the tails" frequency around 30 cm −1 , which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction. © 2014 AIP Publishing LLC.

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Section: Computational Detailssupporting

confidence: 88%

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

Yang

Calero

Martı́

2014

The Journal of Chemical Physics

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“…Using this number, an average condensed-phased area per lipid head group in the Nanodisc of ~60 A 2 can also be estimated, assuming that each leaflet has a diameter of 2 nm smaller than the diameter of the assembly [58]. This result agrees well with previous computational simulations of model DPPC bilayers [64]. …”

Section: Resultssupporting

confidence: 83%

Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

Cleary

Bagal

et al. 2018

J. Am. Soc. Mass Spectrom.

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Native mass spectra of large, polydisperse biomolecules with repeated subunits, such as lipoprotein Nanodiscs, can often be challenging to analyze by conventional methods. The presence of tens of closely spaced, overlapping peaks in these mass spectra can make charge state, total mass, or subunit mass determinations difficult to measure by traditional methods. Recently, we introduced a Fourier Transform-based algorithm that can be used to deconvolve highly congested mass spectra for polydisperse ion populations with repeated subunits and facilitate identification of the charge states, subunit mass, charge-state-specific, and total mass distributions present in the ion population. Here, we extend this method by investigating the advantages of using overtone peaks in the Fourier spectrum, particularly for mass spectra with low signal-to-noise and poor resolution. This method is illustrated for lipoprotein Nanodisc mass spectra acquired on three common platforms, including the first reported native mass spectrum of empty "large" Nanodiscs assembled with MSP1E3D1 and over 300 noncovalently associated lipids. It is shown that overtone peaks contain nearly identical stoichiometry and charge state information to fundamental peaks but can be significantly better resolved, resulting in more reliable reconstruction of charge-state-specific mass spectra and peak width characterization. We further demonstrate how these parameters can be used to improve results from Bayesian spectral fitting algorithms, such as UniDec. Graphical Abstract ᅟ.

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“…For a series of equilibrated MD runs at the NPT ensemble, we have monitored the surface area per lipid considering the total surface along the XY plane (plane parallel to the bilayer surface) divided by the number of lipids plus cholesterol in one lamellar layer. 35 The area per lipid (for the final 70 ns of all trajectories) as a function of simulation times is reported in Fig. 4, and the averaged values are reported in Table I.…”

Section: Resultsmentioning

confidence: 99%

Effects of cholesterol on the binding of the precursor neurotransmitter tryptophan to zwitterionic membranes

Martı́

2018

The Journal of Chemical Physics

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The characterization of the microscopical forces between the essential α-amino-acid tryptophan, precursor of the neurotransmitter serotonin and of the hormone melatonin, and the basic components of cell membranes and their environments (phospholipids, cholesterol, ionic species, and water) is of central importance to elucidate their local structure and dynamics as well as the mechanisms responsible for the access of tryptophan to the interior of the cell. We have performed nanosecond molecular dynamics simulations of tryptophan embedded in model zwitterionic bilayer membranes made by di-palmitoyl-phosphatidyl-choline and cholesterol inside aqueous sodium-chloride solution in order to systematically examine tryptophan-lipid, tryptophan-cholesterol, and tryptophan-water interactions under liquid-crystalline phase conditions. Microscopic properties such as the area per lipid, lipid thickness, radial distribution functions, hydrogen-bonding lengths, atomic spectral densities, and self-diffusion coefficients have been evaluated. Our results show that the presence of tryptophan significantly affects the structure and dynamics of the membrane. Tryptophan spends long periods of time at the water-membrane interface, and it plays a central role by bridging a few lipids and cholesterol chains by means of hydrogen-bonds. The computed spectral densities, in excellent agreement with experimental infrared and Raman data, revealed the participation of each atomic site of tryptophan to the complete spectrum of the molecule. Tryptophan self-diffusion coefficients have been found to be in between 10 −7 and 10 −6 cm 2 /s and strongly depending of the concentration of cholesterol in the system.

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Headgroup Mediated Water Insertion into the DPPC Bilayer: A Molecular Dynamics Study

Cited by 36 publications

References 52 publications

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

Extracting Charge and Mass Information from Highly Congested Mass Spectra Using Fourier-Domain Harmonics

Effects of cholesterol on the binding of the precursor neurotransmitter tryptophan to zwitterionic membranes

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