Exploring the Properties of Curved Lipid Membranes: Comparative Analysis of Atomistic and Coarse-Grained Force Fields

被引:0
|
作者
Domanska, Maria [1 ]
Setny, Piotr [1 ]
机构
[1] Univ Warsaw, Ctr New Technol, Warsaw, Poland
来源
JOURNAL OF PHYSICAL CHEMISTRY B | 2024年 / 128卷 / 29期
关键词
MOLECULAR-DYNAMICS; POTENTIAL FUNCTIONS; LATERAL DIFFUSION; BAR DOMAINS; CURVATURE; CHOLESTEROL; PROTEINS; BILAYERS; MODEL; PHOSPHATIDYLCHOLINE;
D O I
10.1021/acs.jpcb.4c02310
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Curvature emerges as a fundamental membrane characteristic crucial for diverse biological processes, including vesicle formation, cell signaling, and membrane trafficking. Increasingly valuable insights into atomistic details governing curvature-dependent membrane properties are provided by computer simulations. Nevertheless, the underlying force field models are conventionally calibrated and tested in relation to experimentally derived parameters of planar bilayers, thereby leaving uncertainties concerning their consistency in reproducing curved lipid systems. In this study we compare the depiction of buckled phosphatidylcholine (POPC) and POPC-cholesterol membranes by four popular force field models. Aside from agreement with respect to general trends in curvature dependence of a number of parameters, we observe a few qualitative differences. Among the most prominent ones is the difference between atomistic and coarse grained force fields in their representation of relative compressibility of the polar headgroup region and hydrophobic lipid core. Through a number of downstream effects, this discrepancy can influence the way in which curvature modulates the behavior of membrane bound proteins depending on the adopted simulation model.
引用
收藏
页码:7160 / 7171
页数:12
相关论文
共 50 条
  • [1] Evaluating Coarse-Grained MARTINI Force-Fields for Capturing the Ripple Phase of Lipid Membranes
    Sharma, Pradyumn
    Desikan, Rajat
    Ayappa, K. Ganapathy
    JOURNAL OF PHYSICAL CHEMISTRY B, 2021, 125 (24): : 6587 - 6599
  • [2] Atomistic and Coarse-Grained Molecular Simulations of Mixed Lamellar/Nonlamellar Lipid Membranes
    Ding, Wei
    Palaiokostas, Michail
    Wang, Wen
    Orsi, Mario
    BIOPHYSICAL JOURNAL, 2016, 110 (03) : 572A - 572A
  • [3] Anomalous lateral diffusion in lipid bilayers observed by molecular dynamics simulations with atomistic and coarse-grained force fields
    Stachura, Slawomir
    Kneller, Gerald R.
    MOLECULAR SIMULATION, 2014, 40 (1-3) : 245 - 250
  • [4] Water Defect and Pore Formation in Atomistic and Coarse-Grained Lipid Membranes: Pushing the Limits of Coarse Graining
    Bennett, W. F. Drew
    Tieleman, D. Peter
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 7 (09) : 2981 - 2988
  • [5] Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites
    Rzepiela, Andrzej J.
    Louhivuori, Martti
    Peter, Christine
    Marrink, Siewert J.
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2011, 13 (22) : 10437 - 10448
  • [6] Developing coarse-grained force fields for PNIPAM single chain from the atomistic model
    Wang, Zilu
    He, Xuehao
    2009 3RD INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1-11, 2009, : 177 - 180
  • [7] Contrastive Learning of Coarse-Grained Force Fields
    Ding, Xinqiang
    Zhang, Bin
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2022, : 6334 - 6344
  • [8] Exploring gas permeability of lipid membranes using coarse-grained molecular dynamics
    Yuan, Huajun
    Jameson, Cynthia J.
    Murad, Sohail
    MOLECULAR SIMULATION, 2009, 35 (10-11) : 953 - 961
  • [9] Baysian calibration of multiple properties for transferable coarse-grained force fields
    Rosch, Thomas
    Patrone, Paul
    Phelan, Frederick
    ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2016, 252
  • [10] Comparison of coarse-grained (MARTINI) and atomistic molecular dynamics simulations of and toxin nanopores in lipid membranes
    Desikan, Rajat
    Patra, Swarna M.
    Sarthak, Kumar
    Maiti, Prabal K.
    Ayappa, K. G.
    JOURNAL OF CHEMICAL SCIENCES, 2017, 129 (07) : 1017 - 1030