TY - JOUR
T1 - Martini 3 Coarse-Grained Force Field for Cholesterol
AU - Borges-Araújo, Luís
AU - Borges-Araújo, Ana C.
AU - Ozturk, Tugba Nur
AU - Ramirez-Echemendia, Daniel P.
AU - Fábián, Balázs
AU - Carpenter, Timothy S.
AU - Thallmair, Sebastian
AU - Barnoud, Jonathan
AU - Ingólfsson, Helgi I.
AU - Hummer, Gerhard
AU - Tieleman, D. Peter
AU - Marrink, Siewert J.
AU - Souza, Paulo C.T.
AU - Melo, Manuel N.
N1 - Funding Information:
We would like to acknowledge all users of the molecular modeling community that tested beta versions of the cholesterol model, in particular the feedback from Lorena Zuzic, Lisbeth Ravnkilde Kjølbye, Mikkel Dahl Andreasen, Gilberto Pereira, Nathalie Reuter, Reza Talandashti, Changjin Huang, Choon-Peng, Christina Athanasiou, Azadeh Alavizargar, Amita Sahoo, Matthias Buck, Syma Khalid, Jeroen Methorst, Herre Jelger Risselada, Alessandro Marchetto, Simone Albani, and Giulia Rossetti. M.N.M. acknowledges the financial support from Fundação para a Ciência e a Tecnologia (fellowship CEECIND/04124/2017 and project MOSTMICRO-ITQB, with references UIDB/04612/2020 and UIDP/04612/2020). L.B.A. and P.C.T.S. acknowledge the computer time on the Jean-Zay and Joliot-Curie Rome clusters of the French National Supercomputing Center (GENCI project number 2022/A0120713456). L.B.A. and P.C.T.S. also acknowledge the support provided by the CNRS and PharmCADD. B.F. thanks the Alexander von Humboldt-Foundation for funding. B.F. and G.H. thank the Max Planck Society for support. S.T. acknowledges access to the HPC clusters FUCHS and GoetheHLR provided by the Center for Scientific Computing at the Goethe University Frankfurt. S.T. thanks the Hessian Ministry of Science and Arts LOEWE program (Center for Multiscale Modeling in Life Sciences, CMMS), the Alfons und Gertrud Kassel foundation, and Dr. Rolf M. Schwiete foundation for funding. S.J.M. acknowledges ERC funding (grant agreement no. 101053661, COMP-O-CELL). D.P.T. acknowledges support from the Natural Sciences and Engineering Research Council (Canada), the Canada Research Chairs Program, and the Digital Research Alliance of Canada. T.N.O., T.S.C., and H.I.I. thank the Livermore Institutional Grand Challenge for computing time and LDRD 21-ERD-047 for funding. Part of this work was performed under the auspices of the U.S. Department of Energy by the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344, LLNL-JRNL-854111.
Publisher Copyright:
© 2023 American Chemical Society.
PY - 2023/10/24
Y1 - 2023/10/24
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85175585977&partnerID=8YFLogxK
U2 - 10.1021/acs.jctc.3c00547
DO - 10.1021/acs.jctc.3c00547
M3 - Article
C2 - 37796943
AN - SCOPUS:85175585977
SN - 1549-9618
VL - 19
SP - 7387
EP - 7404
JO - Journal Of Chemical Theory And Computation
JF - Journal Of Chemical Theory And Computation
IS - 20
ER -