A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer

Abstract

Infrared (IR) and Raman spectra of a sphingomyelin (SM) bilayer have been calculated for the amide I, II and A modes and the double-bonded CC stretching mode by a weight averaged approach, based on an all-atom molecular dynamics (MD) simulation and a vibrational structure calculation. Representative structures and statistical weights of SM clusters connected by hydrogen bonds (HBs) are observed in MD trajectories. After constructing smaller fragments from the SM clusters, the vibrational spectra of the target modes were calculated by normal mode analysis with a correction for anharmonicity, using density functional theory. The final IR and Raman spectra of a SM bilayer were obtained as the weight averages over all SM clusters. The calculated Raman spectrum is in excellent agreement with a recent measurement, providing a clear assignment of the peak in question observed at 1643 cm(-1) to the amide I modes of a SM bilayer. The analysis of the IR spectrum has also revealed that the amide bands are sensitive to the water content inside the membrane, since their band positions are strongly modulated by the HB between SM and water molecules. The present study suggests that the amide I band serves as a marker to identify the formation of SM clusters, and opens a new way to detect lipid rafts in the biological membrane.

Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers

“…[1,19,51,52] In an impressive recent study, Yagi et al demonstrated the persistency and versatility of hydrogen bonding formation in SM clusters through the interpretation of amide vibrational bands for an SM bilayer. [53] In line with past observations, we observe stable CHOL-SM heterodimers in ternary lipid mixtures (Fig. 10).…”

“…There is substantial support from experimental and computational studies for the importance of hydrogen bonding interaction between CHOL and SM . In an impressive recent study, Yagi et al demonstrated the persistency and versatility of hydrogen bonding formation in SM clusters through the interpretation of amide vibrational bands for an SM bilayer …”

Detection of Sphingomyelin Clusters by Raman Spectroscopy

“…Details of the computational procedure have been given elsewhere (15). An MD simulation of the SM bilayer was conducted using an all-atom force field for SM (16).…”

Weight-Averaged Anharmonic Vibrational Analysis of Hydration Structures of Polyamide 6

“…The method for calculating the IR difference spectrum presented here extends the method suggested in ref . The method is trivially extendable to other systems containing many similar chromophores, for example, other polymer and solvent systems.…”

“…Unlike simple molecular clusters or solids, complex systems have an enormous number of structures (such as H-bond patterns) that contribute to the vibrational spectrum. Recently, we have proposed a weight-averaged approach to calculate the IR and Raman spectra of sphingomyelin (SM) bilayers at different phases. , In this method, molecular dynamics (MD) simulations are first carried out to sample H-bond patterns of amide groups in SM and water molecules. Then, for each pattern, the MD trajectory is used to construct a cluster model, and the harmonic vibrational spectrum is computed using DFT.…”