Martini 3 Coarse-Grained Force Field for Cholesterol

被引：21

作者：

Borges-Araujo, Luis ^{[1
,2
,3
]}

Borges-Araujo, Ana C. ^{[1
]}

Ozturk, Tugba Nur ^{[4
]}

Ramirez-Echemendia, Daniel P. ^{[5
,6
]}

Fabian, Balazs ^{[7
]}

Carpenter, Timothy S. ^{[4
]}

Thallmair, Sebastian ^{[8
]}

Barnoud, Jonathan ^{[9
,10
]}

Ingolfsson, Helgi I. ^{[4
]}

Hummer, Gerhard ^{[7
,11
]}

Tieleman, D. Peter ^{[5
,6
]}

Marrink, Siewert J. ^{[12
]}

Souza, Paulo C. T. ^{[2
,3
]}

Melo, Manuel N. ^{[1
]}

机构：

[1] Univ Nova Lisboa, Inst Tecnol Quim & Biol Antonio Xavier, P-2780157 Oeiras, Portugal

[2] CNRS, UMR 5086, Mol Microbiol & Struct Biochem, F-69367 Lyon, France

[3] Univ Lyon, F-69367 Lyon, France

[4] Lawrence Livermore Natl Lab, Phys & Life Sci PLS Directorate, Livermore, CA 94550 USA

[5] Univ Calgary, Ctr Mol Simulat, Calgary, AB T2N 1N4, Canada

[6] Univ Calgary, Dept Biol Sci, Calgary, AB T2N 1N4, Canada

[7] Max Planck Inst Biophys, Dept Theoret Biophys, D-60438 Frankfurt, Germany

[8] Frankfurt Inst Adv Studies, D-60438 Frankfurt, Germany

[9] Univ Bristol, Ctr Computat Chem, Sch Chem, Bristol BS8 1TS, England

[10] Univ Santiago de Compostela, CiTIUS Intelligent Technol Res Ctr, Santiago De Compostela 15705, Spain

[11] Goethe Univ Frankfurt, Inst Biophys, D-60438 Frankfurt, Germany

[12] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Nijenborgh 7, NL-9747 AG Groningen, Netherlands

来源：

JOURNAL OF CHEMICAL THEORY AND COMPUTATION | 2023年 / 19卷 / 20期

基金：

加拿大自然科学与工程研究理事会;

关键词：

INTERACTION SITES; BINDING-SITES; PHASE-DIAGRAM; BETA(2)-ADRENERGIC RECEPTOR; COMPUTATIONAL LIPIDOMICS; PROTEIN INTERACTIONS; MOLECULAR-STRUCTURE; SOFTWARE NEWS; DYNAMICS; SIMULATIONS;

D O I：

10.1021/acs.jctc.3c00547

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：

Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.

引用

页码：7387 / 7404

页数：18

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