Literature DB >> 22136112

Update of the cholesterol force field parameters in CHARMM.

Joseph B Lim1, Brent Rogaski, Jeffery B Klauda.   

Abstract

A modification of the CHARMM36 lipid force field (C36) for cholesterol, henceforth, called C36c, is reported. A fused ring compound, decalin, was used to model the steroid section of cholesterol. For decalin, C36 inaccurately predicts the heat of vaporization (~10 kJ/mol) and molar volume (~10 cc/mol), but C36c resulted in near perfect comparison with experiment. MD simulations of decalin and heptane at various compositions were run to estimate the enthalpy and volumes of mixing to compare to experiment for this simple model of cholesterol in a chain environment. Superior estimates for these thermodynamic properties were obtained with C36c versus C36. These new parameters were applied to cholesterol, and quantum mechanical calculations were performed to modify the torsional potential of an acyl chain torsion for cholesterol. This model was tested through simulations of DMPC/10% cholesterol, DMPC/30% cholesterol, and DOPC/10% cholesterol. The C36 and C36c results were similar for surface areas per lipid, deuterium order parameters, electron density profiles, and atomic form factors and generally agree well with experiment. However, C36 and C36c produced slightly different cholesterol angle distributions with C36c adopting a more perpendicular orientation with respect to the bilayer plane. The new parameters in the C36c modification should enable more accurate simulations of lipid bilayers with cholesterol, especially for those interested in the free energy of lipid flip/flop or transfer of phospholipids and/or cholesterol.

Entities:  

Mesh:

Substances:

Year:  2011        PMID: 22136112     DOI: 10.1021/jp207925m

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


  56 in total

1.  Identification of novel cholesterol-binding regions in Kir2 channels.

Authors:  Avia Rosenhouse-Dantsker; Sergei Noskov; Serdar Durdagi; Diomedes E Logothetis; Irena Levitan
Journal:  J Biol Chem       Date:  2013-09-09       Impact factor: 5.157

2.  Correction to "Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213".

Authors:  Ilia G Denisov; Yelena V Grinkova; Prithviraj Nandigrami; Mrinal Shekhar; Emad Tajkhorshid; Stephen G Sligar
Journal:  Biochemistry       Date:  2019-06-06       Impact factor: 3.162

Review 3.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

4.  Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture.

Authors:  Asanga Bandara; Afra Panahi; George A Pantelopulos; Tetsuro Nagai; John E Straub
Journal:  J Chem Phys       Date:  2019-05-28       Impact factor: 3.488

5.  A predicted binding site for cholesterol on the GABAA receptor.

Authors:  Jérôme Hénin; Reza Salari; Sruthi Murlidaran; Grace Brannigan
Journal:  Biophys J       Date:  2014-05-06       Impact factor: 4.033

6.  Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions.

Authors:  Fotis A Baltoumas; Margarita C Theodoropoulou; Stavros J Hamodrakas
Journal:  J Comput Aided Mol Des       Date:  2016-06-27       Impact factor: 3.686

7.  Computer simulations of protein-membrane systems.

Authors:  Jennifer Loschwitz; Olujide O Olubiyi; Jochen S Hub; Birgit Strodel; Chetan S Poojari
Journal:  Prog Mol Biol Transl Sci       Date:  2020-02-26       Impact factor: 3.622

8.  Spatially Resolving the Condensing Effect of Cholesterol in Lipid Bilayers.

Authors:  Felix Leeb; Lutz Maibaum
Journal:  Biophys J       Date:  2018-11-02       Impact factor: 4.033

9.  A GIPC1-Palmitate Switch Modulates Dopamine Drd3 Receptor Trafficking and Signaling.

Authors:  Margarita Arango-Lievano; Ozge Sensoy; Amélie Borie; Maithé Corbani; Gilles Guillon; Pierre Sokoloff; Harel Weinstein; Freddy Jeanneteau
Journal:  Mol Cell Biol       Date:  2016-01-19       Impact factor: 4.272

10.  A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.

Authors:  Reza Salari; Thomas Joseph; Ruchi Lohia; Jérôme Hénin; Grace Brannigan
Journal:  J Chem Theory Comput       Date:  2018-11-13       Impact factor: 6.006

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.