Literature DB >> 31574222

Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers.

Hanne Antila1, Pavel Buslaev2, Fernando Favela-Rosales3, Tiago M Ferreira4, Ivan Gushchin2, Matti Javanainen5, Batuhan Kav1, Jesper J Madsen6,7, Josef Melcr5,8, Markus S Miettinen1, Jukka Määttä9, Ricky Nencini5, O H Samuli Ollila5,10, Thomas J Piggot11.   

Abstract

Phosphatidylserine (PS) is a negatively charged lipid type commonly found in eukaryotic membranes, where it interacts with proteins via nonspecific electrostatic interactions as well as via specific binding. Moreover, in the presence of calcium ions, PS lipids can induce membrane fusion and phase separation. Molecular details of these phenomena remain poorly understood, partly because accurate models to interpret the experimental data have not been available. Here we gather a set of previously published experimental NMR data of C-H bond order parameter magnitudes, |SCH|, for pure PS and mixed PS:PC (phosphatidylcholine) lipid bilayers and augment this data set by measuring the signs of SCH in the PS headgroup using S-DROSS solid-state NMR spectroscopy. The augmented data set is then used to assess the accuracy of the PS headgroup structures in, and the cation binding to, PS-containing membranes in the most commonly used classical molecular dynamics (MD) force fields including CHARMM36, Lipid17, MacRog, Slipids, GROMOS-CKP, Berger, and variants. We show large discrepancies between different force fields and that none of them reproduces the NMR data within experimental accuracy. However, the best MD models can detect the most essential differences between PC and PS headgroup structures. The cation binding affinity is not captured correctly by any of the PS force fields-an observation that is in line with our previous results for PC lipids. Moreover, the simulated response of the PS headgroup to bound ions can differ from experiments even qualitatively. The collected experimental data set and simulation results will pave the way for development of lipid force fields that correctly describe the biologically relevant negatively charged membranes and their interactions with ions. This work is part of the NMRlipids open collaboration project ( nmrlipids.blogspot.fi ).

Entities:  

Year:  2019        PMID: 31574222     DOI: 10.1021/acs.jpcb.9b06091

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  10 in total

1.  Calcium-Lipid Interactions Observed with Isotope-Edited Infrared Spectroscopy.

Authors:  Mason L Valentine; Alfredo E Cardenas; Ron Elber; Carlos R Baiz
Journal:  Biophys J       Date:  2020-04-21       Impact factor: 4.033

2.  Lipid headgroup and side chain architecture determine manganese-induced dose dependent membrane rigidification and liposome size increase.

Authors:  Kevin Sule; Elmar J Prenner
Journal:  Eur Biophys J       Date:  2022-02-15       Impact factor: 1.733

3.  In Silico Prediction of the Binding, Folding, Insertion, and Overall Stability of Membrane-Active Peptides.

Authors:  Nicolas Frazee; Violeta Burns; Chitrak Gupta; Blake Mertz
Journal:  Methods Mol Biol       Date:  2021

4.  Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Authors:  Yalun Yu; Andreas Krämer; Richard M Venable; Andrew C Simmonett; Alexander D MacKerell; Jeffery B Klauda; Richard W Pastor; Bernard R Brooks
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

5.  Using Open Data to Rapidly Benchmark Biomolecular Simulations: Phospholipid Conformational Dynamics.

Authors:  Hanne S Antila; Tiago M Ferreira; O H Samuli Ollila; Markus S Miettinen
Journal:  J Chem Inf Model       Date:  2021-01-26       Impact factor: 4.956

6.  Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules.

Authors:  W F Drew Bennett; Stephen J Fox; Delin Sun; C Mark Maupin
Journal:  Membranes (Basel)       Date:  2022-03-22

7.  Charged Small Molecule Binding to Membranes in MD Simulations Evaluated against NMR Experiments.

Authors:  Ricky Nencini; O H Samuli Ollila
Journal:  J Phys Chem B       Date:  2022-09-05       Impact factor: 3.466

8.  Accurate Biomolecular Simulations Account for Electronic Polarization.

Authors:  Josef Melcr; Jean-Philip Piquemal
Journal:  Front Mol Biosci       Date:  2019-12-04

9.  Optimization of Slipids Force Field Parameters Describing Headgroups of Phospholipids.

Authors:  Fredrik Grote; Alexander P Lyubartsev
Journal:  J Phys Chem B       Date:  2020-09-25       Impact factor: 2.991

10.  Lipid21: Complex Lipid Membrane Simulations with AMBER.

Authors:  Callum J Dickson; Ross C Walker; Ian R Gould
Journal:  J Chem Theory Comput       Date:  2022-02-03       Impact factor: 6.006

  10 in total

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