NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics

Shintani, Megumi; Yoshida, Ken; Sakuraba, Shun; Nakahara, Masaru; Matubayasi, Nobuyuki

doi:10.1021/jp204051f

Cited by 15 publications

(20 citation statements)

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“…Artificial lipid bilayers are frequently used as models of cell membranes for investigation of membrane properties and in studies of transmembrane proteins. Although a good deal is known about the structure of artificial membranes (6)(7)(8)(9)(10)(11)(12) and orientational and translational diffusion of lipids and other molecules (7,(13)(14)(15)(16), much less is known about the fast interior structural dynamics of the bilayers, which serve as the dynamic bath modes that can impact membrane processes.…”

mentioning

confidence: 99%

“…However, the results of various studies are not always consistent. Some groups have shown that curvature (vesicle size) does not influence the rates of lipid motions (26)(27)(28)(29) whereas others have provided evidence that there are significant changes with vesicle diameter (14)(15)(16). These are complex experiments, particularly when they recover information on ultrafast time scales that reflect structural fluctuations in contrast to slower processes of translational and orientational diffusion.…”

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confidence: 99%

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Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes

Kel

Tamimi

Fayer

2014

Proc. Natl. Acad. Sci. U.S.A.

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The ultrafast structural dynamics inside the bilayers of dilauroylphosphatidylcholine (DLPC) and dipalmitoylphosphatidylcholine vesicles with 70, 90, and 125 nm diameters were directly measured with 2D IR vibrational echo spectroscopy. The antisymmetric CO stretch of tungsten hexacarbonyl was used as a vibrational probe and provided information on spectral diffusion (structural dynamics) in the alkyl region of the bilayers. Although the CO stretch absorption spectra remain the same, the interior structural dynamics become faster as the size of the vesicles decrease, with the size dependence greater for dipalmitoylphosphatidylcholine than for DLPC. As DLPC vesicles become larger, the interior dynamics approach those of the planar bilayer.vesicle bilayer dynamics | vesicle size dependent dynamics | vesicles chainlength dependent dynamics T he plasma membrane provides a boundary between a living cell and its surroundings and between cellular compartments, providing organizational control of proteins and small molecules that are critical for achieving the complexity of biological systems. In addition to a permeability barrier, the second role of the plasma membrane is serving as the solvent for membrane proteins and other biomolecules. The lipid environment of membrane proteins can influence their function (1-5), and so impact cell signaling, metabolism, growth, defense, and a myriad of other biological functions.Membranes have a bilayer structure where the nonpolar chains of the lipids form the interior of bilayer, with zwitterionic or ionic head groups at the interfaces with water. Artificial lipid bilayers are frequently used as models of cell membranes for investigation of membrane properties and in studies of transmembrane proteins. Although a good deal is known about the structure of artificial membranes (6-12) and orientational and translational diffusion of lipids and other molecules (7, 13-16), much less is known about the fast interior structural dynamics of the bilayers, which serve as the dynamic bath modes that can impact membrane processes.Unilamellar vesicles (ULVs) of different sizes, as well as multilamellar vesicles (MLVs), are used as model membranes owing to their ease of preparation and handling. It has been shown that their properties depend on the curvature (size) (8,9,13,(17)(18)(19)(20). Aligned planar multi-bilayers (21) are membrane models that do not have curvature, yet they are less attractive for routine use because they are substantially more difficult to prepare than vesicles.Numerous experiments have been performed to determine which type of model bilayers most closely represents the properties of the plasma membrane. However, no consensus exists because the results obtained by different methods and groups are not in agreement. Some small-angle X-ray scattering and small-angle neutron scattering (SANS) experiments indicate that the structural properties of ULVs and MLVs are curvature independent, the overall bilayer thickness does not dependent on vesicle size, and the thicknesses of...

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confidence: 99%

mentioning

confidence: 99%

Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes

Kel

Tamimi

Fayer

2014

Proc. Natl. Acad. Sci. U.S.A.

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“…7). SUV shows low packing efficiency among lipids (i.e., packing defects) [78, 88, 109–112], which may provide inhomogeneous hydrophobic clefts in the lipid bilayer [76, 78, 110]. In contrast, LUV shows fewer packing defects and lower hydrophobicity [48, 88, 111].…”

Section: Aggregation Of Amyloid β Peptides In Membrane Environmentsmentioning

confidence: 99%

Impact of membrane curvature on amyloid aggregation

Terakawa

Lin

Kinoshita

et al. 2018

Biochimica et Biophysica Acta (BBA) - Biomembranes

100

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The misfolding, amyloid aggregation, and fibril formation of intrinsically disordered proteins/peptides (or amyloid proteins) have been shown to cause a number of disorders. The underlying mechanisms of amyloid fibrillation and structural properties of amyloidogenic precursors, intermediates, and amyloid fibrils have been elucidated in detail; however, in-depth examinations on physiologically relevant contributing factors that induce amyloidogenesis and lead to cell death remain challenging. A large number of studies have attempted to characterize the roles of biomembranes on protein aggregation and membrane-mediated cell death by designing various membrane components, such as gangliosides, cholesterol, and other lipid compositions, and by using various membrane mimetics, including liposomes, bicelles, and different types of lipid-nanodiscs. We herein review the dynamic effects of membrane curvature on amyloid generation and the inhibition of amyloidogenic proteins and peptides, and also discuss how amyloid formation affects membrane curvature and integrity, which are key for understanding relationships with cell death. Small unilamellar vesicles with high curvature and large unilamellar vesicles with low curvature have been demonstrated to exhibit different capabilities to induce the nucleation, amyloid formation, and inhibition of amyloid-β peptides and α-synuclein. Polymorphic amyloidogenesis in small unilamellar vesicles was revealed and may be viewed as one of the generic properties of interprotein interaction-dominated amyloid formation. Several mechanical models and phase diagrams are comprehensively shown to better explain experimental findings. The negative membrane curvature-mediated mechanisms responsible for the toxicity of pancreatic β cells by the amyloid aggregation of human islet amyloid polypeptide (IAPP) and binding of the precursors of the semen-derived enhancer of viral infection (SEVI) are also described. The curvature-dependent binding modes of several types of islet amyloid polypeptides with high-resolution NMR structures are also discussed.

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“…However, this effect is nonspecific among different types of spin pairs and could be eliminated analogously to the overall molecular tumbling in case of the intramolecular NOE. 12,[16][17][18][19][20] A rather elaborate analysis was recently performed by Shintani et al, 21 who have investigated the dynamics in membranes/micelles. The investigation of these characteristic properties of the intermolecular NOE is the topic of this paper.…”

Section: Is Usedmentioning

confidence: 99%

The intermolecular NOE is strongly influenced by dynamics

Braun

Steinhauser

2015

Phys. Chem. Chem. Phys.

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The intermolecular NOE in NMR spectroscopy is analyzed theoretically via computer simulation. Our test case is the homonuclear NOE between hydrogens in the ionic liquid 1-ethyl-3-methylimidazolium trifluoromethanesulfonate. A coarse-grained model of this system is developed and simulated in a 3 microseconds molecular dynamics run, subsequently used for analysis. Our findings are the following: Spin pair specific dynamics has a strong influence on the spectrum. As a consequence, structural information cannot be read off directly. Instead, different contributions to the signals must be disentangled before one can gain information about structure. We show that the extent of signal distortion through dynamics correlates with the spins' distance to their respective molecular centers of mass. Since we deal with pair distributions of spins, the extracted structure does not represent average distances between two spins but the sum of the influence of surrounding spins. In fact, we find that this influence is long-ranged. Our data explicitly shows that the usual 1/r(6) dependence is replaced by a distance dependence between 1/r(3) and 1/r. However, structural information consists of a spin pair specific short-ranged contribution and a uniform long-ranged contribution. The transition from specific to uniform is sensitive to the behavior of the underlying pair distribution functions.

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NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics

Cited by 15 publications

References 79 publications

Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes

Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes

Impact of membrane curvature on amyloid aggregation

The intermolecular NOE is strongly influenced by dynamics

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