Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

Milka Doktorova; Norbert Kučerka; Jacob J. Kinnun; Jianjun Pan; Drew Marquardt; Haden L. Scott; Richard M. Venable; Richard W. Pastor; Stephen R. Wassall; John Katsaras; Frederick A. Heberle

doi:10.1021/acs.jpcb.0c03389

Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

Milka Doktorova, Norbert Kučerka, Jacob J. Kinnun, Jianjun Pan, Drew Marquardt, Haden L. Scott, Richard M. Venable, Richard W. Pastor, Stephen R. Wassall, John Katsaras, Frederick A. Heberle

Labs & Soft Matter

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21 Scopus citations

Abstract

We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.

Original language	English
Pages (from-to)	5186-5200
Number of pages	15
Journal	Journal of Physical Chemistry B
Volume	124
Issue number	25
DOIs	https://doi.org/10.1021/acs.jpcb.0c03389
State	Published - Jun 25 2020

Funding

We thank the following: Venky Pingali, Shuo Qian, and Chris Stanley for assistance with SANS measurements; Arthur Woll for assistance with SAXS measurements; and Boris Dzikovski for assistance with ESR data collection. F.A.H. and H.L.S. were supported by National Science Foundation (NSF) Grant No. MCB-1817929 (to F.A.H.). M.D. was supported by National Institutes of Health (NIH) Grant No. 1F32GM134704-01. The computational work used the Extreme Science and Engineering Discovery Environment (XSEDE), accounts TG-MCB160016, TG-MCB160018, and TG-MCB130010. A portion of this research used resources from the CG3 BioSANS instrument at the High Flux Isotope Reactor and the EQ-SANS instrument at the Spallation Neutron Source, both Department of Energy (DOE) Office of Science user facilities operated by Oak Ridge National Laboratory (ORNL) under contract number DEAC05-00OR22725. Synchrotron SAXS data were collected at the Cornell High Energy Synchrotron Source (CHESS), which is supported by the NSF and the NIH/National Institute of General Medical Sciences under NSF award DMR-0936384. BioSAXS measurements were supported by DOE scientific user facilities at ORNL. Additional measurements were supported by the Biophysical Characterization Suite of the Shull Wollan Center at ORNL. ESR measurements were conducted at the National Biomedical Center for Advanced ESR Technology at Cornell University.

Funders	Funder number
National Science Foundation	MCB-1817929
National Institutes of Health
U.S. Department of Energy
National Institute of General Medical Sciences	DMR-0936384, F32GM134704
Oak Ridge National Laboratory	DEAC05-00OR22725

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Doktorova, M., Kučerka, N., Kinnun, J. J., Pan, J., Marquardt, D., Scott, H. L., Venable, R. M., Pastor, R. W., Wassall, S. R., Katsaras, J., & Heberle, F. A. (2020). Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data. Journal of Physical Chemistry B, 124(25), 5186-5200. https://doi.org/10.1021/acs.jpcb.0c03389

@article{b26cbbbadfef44f39697343388ff9fe8,

title = "Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data",

abstract = "We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 {\AA}2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 {\AA}2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 {\AA}2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.",

author = "Milka Doktorova and Norbert Ku{\v c}erka and Kinnun, {Jacob J.} and Jianjun Pan and Drew Marquardt and Scott, {Haden L.} and Venable, {Richard M.} and Pastor, {Richard W.} and Wassall, {Stephen R.} and John Katsaras and Heberle, {Frederick A.}",

note = "Publisher Copyright: Copyright {\textcopyright} 2020 American Chemical Society.",

year = "2020",

month = jun,

day = "25",

doi = "10.1021/acs.jpcb.0c03389",

language = "English",

volume = "124",

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issn = "1520-6106",

publisher = "American Chemical Society",

number = "25",

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Doktorova, M, Kučerka, N, Kinnun, JJ, Pan, J, Marquardt, D, Scott, HL, Venable, RM, Pastor, RW, Wassall, SR, Katsaras, J & Heberle, FA 2020, 'Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data', Journal of Physical Chemistry B, vol. 124, no. 25, pp. 5186-5200. https://doi.org/10.1021/acs.jpcb.0c03389

TY - JOUR

T1 - Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

AU - Doktorova, Milka

AU - Kučerka, Norbert

AU - Kinnun, Jacob J.

AU - Pan, Jianjun

AU - Marquardt, Drew

AU - Scott, Haden L.

AU - Venable, Richard M.

AU - Pastor, Richard W.

AU - Wassall, Stephen R.

AU - Katsaras, John

AU - Heberle, Frederick A.

PY - 2020/6/25

Y1 - 2020/6/25

N2 - We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.

AB - We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.

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AN - SCOPUS:85087110560

SN - 1520-6106

VL - 124

SP - 5186

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JO - Journal of Physical Chemistry B

JF - Journal of Physical Chemistry B

IS - 25

ER -

Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

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