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  1. Article ; Online: Binding of Cholesterol to the N-Terminal Domain of the NPC1L1 Transporter: Analysis of the Epimerization-Related Binding Selectivity and Loop Mutations.

    Valdivia, Aitor / Luque, F Javier / Llabrés, Salomé

    Journal of chemical information and modeling

    2023  Volume 64, Issue 1, Page(s) 189–204

    Abstract: Cholesterol is a fat-like substance with a pivotal physiological relevance in humans, and its homeostasis is tightly regulated by various cellular processes, including the import in the small intestine and the reabsorption in the biliary ducts by the ... ...

    Abstract Cholesterol is a fat-like substance with a pivotal physiological relevance in humans, and its homeostasis is tightly regulated by various cellular processes, including the import in the small intestine and the reabsorption in the biliary ducts by the Niemann-Pick C1 Like 1 (NPC1L1) importer. NPC1L1 can mediate the absorption of a variety of sterols but strikingly exhibits a large sensitivity to cholesterol epimerization. This study examines the molecular basis of the epimerization-related selective binding of cholesterol by combining extended unbiased molecular dynamics simulations of the apo and holo species of the N-terminal domain of wild-type NPC1L1, in conjunction with relative binding free energy, umbrella sampling, and well-tempered metadynamics calculations. The analysis of the results discloses the existence of two distinct binding modes for cholesterol and epi-cholesterol. The former binds deeper in the cavity, forming key hydrogen-bond interactions with Q95, S56, and a water molecule. In contrast, epi-cholesterol is shifted ca. 3 Å to the mouth of the cavity and the transition to the Q95 site is prevented by an energetic barrier of 4.1 kcal·mol
    MeSH term(s) Humans ; Membrane Proteins/chemistry ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Cholesterol/metabolism ; Mutation ; Water/metabolism
    Chemical Substances Membrane Proteins ; Membrane Transport Proteins ; Cholesterol (97C5T2UQ7J) ; Water (059QF0KO0R) ; NPC1L1 protein, human
    Language English
    Publishing date 2023-12-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c01319
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Carbon nanotube transmembrane channel formation and single-stranded DNA spontaneous internalization: a dissipative particle dynamics study.

    Valdivia, Aitor / Jaime, Carlos

    Soft matter

    2020  Volume 17, Issue 4, Page(s) 1028–1036

    Abstract: Single-walled carbon nanotube (SWCNT) transmembrane channel formation in a pure 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) bilayer, and the spontaneous internalization of single-stranded DNA (ssDNA) into the formed pore were simulated. A ... ...

    Abstract Single-walled carbon nanotube (SWCNT) transmembrane channel formation in a pure 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) bilayer, and the spontaneous internalization of single-stranded DNA (ssDNA) into the formed pore were simulated. A combination of computational techniques, Dissipative Particle Dynamics-Monte Carlo hybrid simulations and quantum mechanical calculations at the hybrid-DFT level, was used as a new proposal to perform DPD simulations granting specific chemical identity to the model particles. The simulated transmembrane channels showed that, in the case of pristine SWCNTs and upon increasing the nanotube length, a higher tilt angle with respect to the bilayer normal is observed and more time is needed for the nanotube to stabilize. On the other hand, for SWCNTs with polar rims an almost perpendicular orientation is preferred with less than 15° of tilt with respect to the bilayer normal once the nanotubes have pierced both monolayers. These findings are supported by experimental observations where CNTs of average inner diameters of 1.51 ± 0.21 nm and lengths in the 5-15 nm range were inserted in DOPC membranes [J. Geng, et al., Nature, 2014, 514(7524), 612-615]. Moreover, the narrower the SWCNTs, the slower the spontaneous internalization of ssDNA becomes, and ssDNA ends hydrophobically trapped inside the artificial pore. A dependence on the nucleotide content is found indicating that the higher the presence of adenine and thymine in the ssDNA chains the slower the internalization becomes, in agreement with the experimental [A. M. Ababneh, et al., Biophys. J., 2003, 85(2), 1111-1127] and predicted solvation tendency in water for nucleic acid bases.
    MeSH term(s) DNA, Single-Stranded ; Nanotubes, Carbon ; Water
    Chemical Substances DNA, Single-Stranded ; Nanotubes, Carbon ; Water (059QF0KO0R)
    Language English
    Publishing date 2020-12-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2191476-X
    ISSN 1744-6848 ; 1744-683X
    ISSN (online) 1744-6848
    ISSN 1744-683X
    DOI 10.1039/d0sm01615b
    Database MEDical Literature Analysis and Retrieval System OnLINE

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