Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models

Srivastava, Abhinav; Malik, Sheeba; Debnath, Ananya

doi:10.1016/j.chemphys.2019.110396

Cited by 20 publications

(19 citation statements)

References 77 publications

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“…All-atom molecular dynamics simulations were performed using the GROMACS-4.5.6 package. − Four bilayers were set up with two lipid compositions, DMPC and DMPG each at 0 and 5 mol % DMSO and 128 lipids as shown in Figure S2 and Table S1. All systems were hydrated with the TIP4P/2005 water model. − Thus, ∼45 water molecules per lipid were present in our system. Slipid and the GAFF force field were used for the lipids and DMSO, respectively. − Concentrations were calculated on the basis of the mole percent of DMSO .…”

Section: Experimental Sectionmentioning

confidence: 99%

A Comparative Study on DMSO-Induced Modulation of the Structural and Dynamical Properties of Model Bilayer Membranes

et al. 2021

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Modulating the structures and properties of biomembranes via permeation of small amphiphilic molecules is immensely important, having diverse applications in cell biology, biotechnology, and pharmaceuticals, because their physiochemical and biological interactions lead to new pathways for transdermal drug delivery and administration. In this work, we have elucidated the role of dimethyl sulfoxide (DMSO), broadly used as a penetration-enhancing agent and cryoprotective agent on model lipid membranes, using a combination of fluorescence microscopy and time-resolved fluorescence spectroscopy. Spatially resolved fluorescence lifetime imaging microscopy (FLIM) has been employed to unravel how the fluidity of the DMSO-induced bilayer regulates the structural alteration of the vesicles. Moreover, we have also shown that the dehydration effect of DMSO leads to weakening of the hydrogen bond between lipid headgroups and water molecules and results in faster solvation dynamics as demonstrated by femtosecond time-resolved fluorescence spectroscopy. It has been gleaned that the water dynamics becomes faster because bilayer rigidity decreases in the presence of DMSO, which is also supported by time-resolved rotational anisotropy measurements. The enhanced diffusivity and increased membrane fluidity in the presence of DMSO are further ratified at the single-molecule level through fluorescence correlation spectroscopy (FCS) measurements. Our results indicate that while the presence of DMSO significantly affects the 1,2-dimyristoyl-rac-glycero-3-phosphocholine (DMPC) and 1,2-dipalmitoyl-rac-glycero-3-phosphatidylcholine (DPPC) bilayers, it has a weak effect on 1,2-dimyristoyl-sn-glycero-3-phospho-rac-glycerol (DMPG) vesicles, which might explain the preferential interaction of DMSO with the positively charged choline group present in DMPC and DPPC vesicles. The experimental findings have also been further verified with molecular dynamics simulation studies. Moreover, it has been observed that DMSO is likely to have a differential effect on heterogeneous bilayer membranes depending on the structure and composition of their headgroups. Our results illuminate the importance of probing the lipid structure and composition of cellular membranes in determining the effects of cryoprotective agents.

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Section: Experimental Sectionmentioning

confidence: 99%

A Comparative Study on DMSO-Induced Modulation of the Structural and Dynamical Properties of Model Bilayer Membranes

et al. 2021

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“…All-atom molecular dynamics simulations are carried out using the GROMACS-4.5.6 package. , Four single bilayers are set up with different lipid types, 1,2-dimyristoyl- sn -glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl- sn -glycero-3-phosphocholine (POPC) and their mixtures with different hydration numbers (S1–S4 shown in Table ). Four DMPC multibilayers are set up by varying the hydration numbers from 10 to 18, 26, and 44 (S5–S8 shown in Table ). All systems are solvated with the TIP4P/2005 water model.…”

Section: Experimental and Theoretical Sectionmentioning

confidence: 99%

“…Initially 128 DMPC lipids with the CHARMM36 force field , are solvated with 5743 TIP4P/2005 water molecules (S1 in Table ) as this is the fully hydrated state using a previously equilibrated DMPC system at 308 K . Combination of CHARMM36 force fields of the bilayer in the presence of the TIP4P/2005 water model is found to reproduce the experimental dynamical properties of water keeping the membrane fluid phase intact .…”

Section: Experimental and Theoretical Sectionmentioning

confidence: 99%

“…32,33 Four single bilayers are set up with different lipid types, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2oleoyl-sn-glycero-3-phosphocholine (POPC) and their mixtures with different hydration numbers (S1−S4 shown in Table 1). Four DMPC multibilayers are set up by varying the hydration numbers 17 1) as this is the fully hydrated state using a previously equilibrated DMPC system at 308 K. 17 Combination of CHARMM36 force fields of the bilayer in the presence of the TIP4P/2005 water model is found to reproduce the experimental dynamical properties of water keeping the membrane fluid phase intact. 17 The area per headgroup, bilayer thickness, and order parameter for the DMPC bilayer using the CHARMM36 force fields match previously performed computational data 17,37 as well as the experimental data.…”

Section: ■ Introductionmentioning

confidence: 99%

“…During the past few decades, several research laboratories have demonstrated the water dynamics at the interfaces of various confined media. They have studied water dynamics inside various model confined systems such as micelles, reverse micelles, fatty acid vesicles, and phospholipid vesicles. − In order to unravel the solvation dynamics in these assemblies, scientists have performed molecular dynamics (MD) simulations − using the coarse-grained model, time-resolved fluorescence spectroscopy, dielectric relaxation, and surface second harmonic generation (SSHG) . In addition, recently extensive efforts have been dedicated to elucidate the collective dynamics of the phospholipid bilayer by means of inelastic X-ray and neutron scattering. − On the above studies, water dynamics predicts the lipid bilayer properties and lipid molecule dynamics anticipates the transportation behavior.…”

Section: Introductionmentioning

confidence: 99%

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Modulation of Membrane Fluidity to Control Interfacial Water Structure and Dynamics in Saturated and Unsaturated Phospholipid Vesicles

et al. 2020

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The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.

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Phonon-mediated lipid raft formation in biological membranes

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et al. 2020

Chemistry and Physics of Lipids

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Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models

Cited by 20 publications

References 77 publications

A Comparative Study on DMSO-Induced Modulation of the Structural and Dynamical Properties of Model Bilayer Membranes

A Comparative Study on DMSO-Induced Modulation of the Structural and Dynamical Properties of Model Bilayer Membranes

Modulation of Membrane Fluidity to Control Interfacial Water Structure and Dynamics in Saturated and Unsaturated Phospholipid Vesicles

Phonon-mediated lipid raft formation in biological membranes

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