Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations

Okabe, Ryo; Ito, Natsuumi; Matsubara, Yuya; Morishita Watanabe, Nozomi; Umakoshi, Hiroshi; Kasahara, Kento; Matubayasi, Nobuyuki

doi:https://doi.org/10.1063/5.0279530

Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations

Okabe, Ryo; Ito, Natsuumi; Matsubara, Yuya et al.

The Journal of Chemical Physics, 2025, 163(3), 034708

Number of Access:113（2025-10-23 01:33 Counts）

Identifier to cite or link to this item: https://hdl.handle.net/11094/102319

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Title	Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations
Creator	CreatorName Okabe, Ryo
	CreatorName Ito, Natsuumi
	CreatorName Matsubara, Yuya
	NRID 1000040892683 1000040892683 ORCID 0000-0002-3461-3660 0000-0002-3461-3660 researchmap permalink nozomiwatanabe nozomiwatanabe Scopus Author ID 57190045741 57190045741 CreatorName Morishita Watanabe, Nozomi
	NRID 1000020311772 1000020311772 researchmap permalink read0191167 read0191167 Scopus Author ID 6701925853 6701925853 CreatorName Umakoshi, Hiroshi
	NRID 1000010824469 1000010824469 ORCID 0000-0001-7138-250X 0000-0001-7138-250X researchmap permalink kasakento kasakento Scopus Author ID 56245700800 56245700800 CreatorName Kasahara, Kento
	NRID 1000020281107 1000020281107 ORCID 0000-0001-7176-441X 0000-0001-7176-441X researchmap permalink nbyk_MTBYS nbyk_MTBYS Scopus Author ID 7003410578 7003410578 CreatorName Matubayasi, Nobuyuki
Description	R. Okabe et al., J. Chem. Phys. 163, 034708 (2025); https://doi.org/10.1063/5.0279530.
Abstract	The physicochemical properties of lipid bilayers (membranes) are closely associated with various cellular functions and are often evaluated using absorption and fluorescence spectroscopies. For instance, by employing fluorescent probes that exhibit spectra reflective of the surrounding membrane environment, one can estimate the membrane polarity. Thus, elucidating how such probes are embedded within the membranes would be beneficial for enabling a deeper interpretation of the spectra. Here, we apply molecular dynamics simulation with an enhanced sampling method to investigate the embedded state of 6-propionyl-2-dimethylaminonaphthalene (Prodan) within a membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine, as well as its variation upon the addition of ethanol as a cosolvent to the aqueous phase. In the absence of ethanol, it is found that the bulky moieties of Prodan (propionyl and dimethylamine groups) prefer to be oriented toward the membrane center owing to the voids existing near the center. The structural change in the membrane induced by the addition of ethanol causes a reduction in the void population near the center, resulting in a diminished orientation preference of Prodan.
Publisher	AIP Publishing
Source Title	The Journal of Chemical Physics
Volume (Issue)	163(3)
Page	034708
Date of Issued	2025-07-16
Language	English
Handle URL	https://hdl.handle.net/11094/102319
PISSN	00219606
eISSN	10897690
Relation.isIdenticalTo	DOI (Publisher Version) https://doi.org/10.1063/5.0279530
Access Rights	embargoed access
CopyRight	This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics 163 (2025) and may be found at https://doi.org/10.1063/5.0279530.
CopyRight	The full-text file will be made open to the public on 16 July 2026 in accordance with the publisher's policy.
oaire:version	Version of Record
Category	学術雑誌論文 Journal Article

Resource Type	journal article
Local Type	Journal Article
DCMI Type	Text
DCTERMS.bibliographicCitation	The Journal of Chemical Physics. 2025, 163(3), p. 034708
DC.title	Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations
DC.creator	Okabe, Ryo
	Ito, Natsuumi
	Matsubara, Yuya
	Morishita Watanabe, Nozomi
	Umakoshi, Hiroshi
	Kasahara, Kento
	Matubayasi, Nobuyuki
DC.publisher	AIP Publishing
DC.language' scheme='DCTERMS.RFC1766	English
DC.type' scheme='DCTERMS.DCMIType	Text
DCTERMS.issued' scheme='DCTERMS.W3CDTF	2025-07-16
DC.identifier	https://doi.org/10.1063/5.0279530
DC.description	R. Okabe et al., J. Chem. Phys. 163, 034708 (2025); https://doi.org/10.1063/5.0279530.
DCTERMS.abstract	The physicochemical properties of lipid bilayers (membranes) are closely associated with various cellular functions and are often evaluated using absorption and fluorescence spectroscopies. For instance, by employing fluorescent probes that exhibit spectra reflective of the surrounding membrane environment, one can estimate the membrane polarity. Thus, elucidating how such probes are embedded within the membranes would be beneficial for enabling a deeper interpretation of the spectra. Here, we apply molecular dynamics simulation with an enhanced sampling method to investigate the embedded state of 6-propionyl-2-dimethylaminonaphthalene (Prodan) within a membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine, as well as its variation upon the addition of ethanol as a cosolvent to the aqueous phase. In the absence of ethanol, it is found that the bulky moieties of Prodan (propionyl and dimethylamine groups) prefer to be oriented toward the membrane center owing to the voids existing near the center. The structural change in the membrane induced by the addition of ethanol causes a reduction in the void population near the center, resulting in a diminished orientation preference of Prodan.
DC.rights	This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics 163 (2025) and may be found at https://doi.org/10.1063/5.0279530.
DC.rights	The full-text file will be made open to the public on 16 July 2026 in accordance with the publisher's policy.
DC.format	102319
citation_title	Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations
citation_author	Okabe, Ryo
	Ito, Natsuumi
	Matsubara, Yuya
	Morishita Watanabe, Nozomi
	Umakoshi, Hiroshi
	Kasahara, Kento
	Matubayasi, Nobuyuki
citation_publisher	AIP Publishing
citation_language	English
citation_date	2025-07-16
citation_journal_title	The Journal of Chemical Physics
citation_volume	163
citation_issue	3
citation_firstpage	034708
citation_doi	https://doi.org/10.1063/5.0279530
citation_public_url	https://hdl.handle.net/11094/102319

Characterizing the embedded states of a fluorescent probe within a lipid bilayer using molecular dynamics simulations

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