Institute of Fundamental Technological Research
Polish Academy of Sciences


K. Okazaki

Recent publications
1.  Poblete S., Pantano S., Okazaki K., Liang Z., Kremer K., Poma Adolfo B., Editorial: Recent advances in computational modelling of biomolecular complexes, Frontiers in Chemistry, ISSN: 2296-2646, DOI: 10.3389/fchem.2023.1200409, Vol.11, pp.1200409-1-3, 2023, EDITORIAL

coarse-grained method, machine learning, multiscale approach, biopolymers, aggregation, GōMartini approach, Martini 3, nanomechanics

Poblete S. - other affiliation
Pantano S. - other affiliation
Okazaki K. - other affiliation
Liang Z. - other affiliation
Kremer K. - other affiliation
Poma Adolfo B. - IPPT PAN
2.  Mahmood I., Poma Bernaola A., Okazaki K., Optimizing Gō-MARTINI coarse-grained model for F-BAR protein on lipid membrane, Frontiers in Molecular Biosciences, ISSN: 2296-889X, DOI: 10.3389/fmolb.2021.619381, Vol.8, pp.619381-1-10, 2021

Coarse-grained (CG) molecular dynamics (MD) simulations allow us to access much larger length and time scales than atomistic MD simulations, providing an attractive alternative to the conventional simulations. Based on the well-known MARTINI CG force field, the recently developed Gō-MARTINI model for proteins describes large-amplitude structural dynamics, which has not been possible with the commonly used elastic network model. Using the Gō-MARTINI model, we conduct MD simulations of the F-BAR Pacsin1 protein on lipid membrane. We observe that structural changes of the non-globular protein are largely dependent on the definition of the native contacts in the Gō model. To address this issue, we introduced a simple cutoff scheme and tuned the cutoff distance of the native contacts and the interaction strength of the Lennard-Jones potentials in the Gō-MARTINI model. With the optimized Gō-MARTINI model, we show that it reproduces structural fluctuations of the Pacsin1 dimer from atomistic simulations. We also show that two Pacsin1 dimers properly assemble through lateral interaction on the lipid membrane. Our work presents a first step towards describing membrane remodeling processes in the Gō-MARTINI CG framework by simulating a crucial step of protein assembly on the membrane.

Gō-MARTINI, protein complex, Pacsin, membrane remodeling, molecular dynamics, principal component analysis, RMSIP, assembly, protein contacts

Mahmood I. - other affiliation
Poma Bernaola A. - IPPT PAN
Okazaki K. - other affiliation

Category A Plus


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