CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation

被引:3
|
作者
Brown, Turner P. [1 ]
Santa, Dane E. [2 ]
Berger, Brett A. [2 ]
Kong, Lingyang [3 ]
Wittenberg, Nathan J. [2 ]
Im, Wonpil [1 ,2 ,3 ]
机构
[1] Lehigh Univ, Dept Bioengn, Bethlehem, PA 18015 USA
[2] Lehigh Univ, Dept Chem, Bethlehem, PA 18015 USA
[3] Lehigh Univ, Dept Biol Sci, Bethlehem, PA 18015 USA
关键词
LIPID-BILAYERS; MOLECULAR-DYNAMICS; FORCE-FIELD; CD36; OXIDATION; RECEPTOR; LIGANDS; PEROXIDATION;
D O I
10.1016/j.sbi.2024.102813
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Oxidative stress leads to the production of oxidized phospholipids (oxPLs) that modulate the biophysical properties of phospholipid monolayers and bilayers. As many immune cells are responsible for surveilling cells and tissues for the presence of oxPLs, oxPL-dependent mechanisms have been suggested as targets for treating chronic kidney disease, atherosclerosis, diabetes, and cancer metastasis. This review details recent experimental and computational studies that characterize oxPLs' behaviors in various monolayers and bilayers. These studies investigate how the tail length and polar functional groups of OxPLs impact membrane properties, how oxidized membranes can be stabilized, and how membrane integrity is generally affected by oxidized lipids. In addition, for oxPL-containing membrane modeling and simulation, CHARMM-GUI Membrane Builder has been extended to support a variety of oxPLs, accelerating the simulation system building process for these biologically relevant lipid bilayers.
引用
收藏
页数:7
相关论文
共 50 条
  • [21] CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates
    Park, Sang-Jun
    Lee, Jumin
    Qi, Yifei
    Kern, Nathan R.
    Lee, Hui Sun
    Jo, Sunhwan
    Joung, InSuk
    Joo, Keehyung
    Lee, Jooyoung
    Im, Wonpil
    GLYCOBIOLOGY, 2019, 29 (04) : 320 - 331
  • [22] CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems
    Choi, Yeol Kyo
    Kern, Nathan R.
    Kim, Seonghan
    Kanhaiya, Krishan
    Afshar, Yaser
    Jeon, Sun Hee
    Jo, Sunhwan
    Brooks, Bernard R.
    Lee, Jumin
    Tadmor, Ellad B.
    Heinz, Hendrik
    Im, Wonpil
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, 18 (01) : 479 - 493
  • [23] CHARMM-GUI multicomponent assembler for modeling and simulation of complex multicomponent systems
    Kern, Nathan R.
    Lee, Jumin
    Choi, Yeol Kyo
    Im, Wonpil
    BIOPHYSICAL JOURNAL, 2022, 121 (03) : 529A - 529A
  • [24] CHARMM-GUI Synthetic Polymer Modeler for Modeling and Simulation of Synthetic Polymers
    Choi, Yeol Kyo
    Duran, Tibo
    Im, Wonpil
    BIOPHYSICAL JOURNAL, 2019, 116 (03) : 572A - 572A
  • [25] CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation
    Kong, Lingyang
    Park, Sang-Jun
    Im, Wonpil
    JOURNAL OF MOLECULAR BIOLOGY, 2024, 436 (17)
  • [26] CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems
    Kern, Nathan R.
    Lee, Jumin
    Choi, Yeol Kyo
    Im, Wonpil
    NATURE COMMUNICATIONS, 2024, 15 (01)
  • [27] CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Heterogeneous Biomolecular Systems
    Kern, Nathan R.
    BIOPHYSICAL JOURNAL, 2019, 116 (03) : 290A - 290A
  • [28] CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides
    Hsu, Pin-Chia
    Bruininks, Bart M. H.
    Jefferies, Damien
    Souza, Paulo Cesar Telles de
    Lee, Jumin
    Patel, Dhilon S.
    Marrink, Siewert J.
    Qi, Yifei
    Khalid, Syma
    Im, Wonpil
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2017, 38 (27) : 2354 - 2363
  • [29] CHARMM-Gui Pace Cg Builder for Solution, Micelle, Bilayer and Vesicle Simulations
    Qi, Yifei
    Cheng, Xi
    Han, Wei
    Jo, Sunhwan
    Roux, Benoit
    Schulten, Klaus
    Im, Wonpil
    BIOPHYSICAL JOURNAL, 2014, 106 (02) : 809A - 809A
  • [30] CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems
    Cheng, Xi
    Jo, Sunhwan
    Lee, Hui Sun
    Klauda, Jeffery B.
    Im, Wonpil
    JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2013, 53 (08) : 2171 - 2180