Recalibration of MARTINI-3 Parameters for Improved Interactions between Peripheral Proteins and Lipid Bilayers

Kinetics and Mechanism of Phase Separation in Ternary Lipid Mixtures Containing APP C99: Atomistic vs Coarse-Grained MD Simulations

The phase separation of lipid bilayers, composed of mixtures of saturated and unsaturated lipids and cholesterol, is a topic of fundamental importance in membrane biophysics and cell biology. The formation of lipid domains, including liquid-disordered domains enriched in unsaturated lipids and liquid-ordered domains enriched in saturated lipids and cholesterol, is believed to be essential to the function of many membrane proteins. Experiment, theory, and simulation have been used to develop a general understanding of the thermodynamic driving forces underlying phase separation in ternary and quaternary lipid mixtures. However, the kinetics of early events in lipid phase separation in the presence of transmembrane proteins remain relatively understudied. Using large-scale all-atom and coarse-grained simulations, we explore the kinetics and phase separation of ternary lipid mixtures of saturated lipid, unsaturated lipid, and cholesterol in the presence of transmembrane proteins. Order parameters employed in the Cahn-Hilliard theory provide insight into the kinetics and mechanism of lipid phase separation. We observe three distinct time regimes in the phase separation process: a shorter exponential time phase, followed by a power-law phase, and then a longer plateau phase. Comparison of lipid, protein, and lipid-protein dynamics between all-atom and coarse-grained models identifies both quantitative and qualitative differences and similarities in the phase separation kinetics. Moreover, timescaling of the dynamics of the AA and CG simulations yields a similar kinetic mechanism of phase separation. The findings of this study elucidate fundamental aspects of membrane biophysics and contribute to ongoing efforts to define the role of lipid rafts in the structure and function of the cellular membrane.

How Are Plastoglobules Formed in Green Algae?

Plastoglobules are droplet-like organelles with a hydrophobic core of neutral lipids surrounded by a lipid monolayer, usually found in the chloroplasts of most plants and green algae. They not only serve as lipid storage units in the thylakoid membranes but are also involved in many cellular processes, including photoprotection, metabolite synthesis, protein recruitment, and chloroplast differentiation. Unlike lipid droplets, which nucleate, grow, and subsequently detach from the endoplasmic reticulum (ER) membrane, plastoglobules remain permanently coupled to the stromal side of the thylakoid membrane. In this study, we employ molecular dynamics simulations to investigate the growth mechanism of plastoglobules in a model thylakoid membrane of Dunaliella algae. Our findings suggest that significant membrane remodeling, likely driven by the thylakoid membrane proteins, is essential for the directional growth and stability of the plastoglobules.

Computational analysis of the structural-functional dynamics of a Co-receptor proteoglycan

Nerve-Glial Antigen 2/Chondroitin Sulphate Proteoglycan 4 (NG2/CSPG4) is the largest membrane-intercalated cell surface component of the human proteome known to date. NG2/CSPG4 is endowed with the capability of engaging a myriad of molecular interactions and exert co-receptor functions, of which primary ones are sequestering of growth factors and the anchoring of cells to the extracellular matrix. However, the nature of the interactive dynamics of the proteoglycan remains veiled because of its conspicuous size and structural complexity. By leveraging on a multi-scale in silico approach, we have pioneered a comprehensive computational analysis of the structural-functional traits of the NG2/CSPG4 ectodomain. The modelling highlights an intricate assembly of β-sheet motifs linked together by flexible loops. Furthermore, our in silico predictions highlight that the previously delineated D1 domain may consistently remain more accessible for molecular interplays with respect to the D2 and D3 domains. Based on these findings, we have simulated the structural mechanism through the proteoglycan may serve as a co-receptor for growth factor FGF-2, showing that NG2/CSPG4 bends towards the receptor FGFR-1 for this growth factor and confirming the previously hypothesized trimeric complex formation promoted by FGF-2 dimers bridging the FGFR-1-proteoglycan interaction. The Chondroitin Sulphate Proteoglycan 4 is a large multi-domain transmembrane protein involved in several biological processes including pathological conditions. Despite its importance, it has never been studied at the atomistic level due to its large size. Here, we employed a multi-scale computer simulations approach to study its three-dimensional structure, its movements and co-receptor properties, showing that it can serve as mediator in the growth factor signaling process.

Benchmarking a dual-scale hybrid simulation framework for small globular proteins combining the CHARMM36 and Martini2 models

Multi-scale models in which varying resolutions are considered in a single molecular dynamics simulation setup are gaining importance in integrative modeling. However, combining atomistic and coarse-grain resolutions, especially for coarse-grain force fields derived from top-down approaches, have not been well explored. In this study, we have implemented and tested a dual-resolution simulation approach to model globular proteins in atomistic detail (represented by the CHARMM36 model) with the surrounding solvent in Martini2 coarse-grain detail. The hybrid scheme considered is an extension of a model implemented earlier for mainly lipid and water molecules. We have considered a set of small globular proteins and have extensively compared to atomistic benchmark simulations as well as a host of experimental observables. We show that the protein structural dynamics sampled in the hybrid scheme is robust, and the intra-protein contact maps are reproduced, despite increased fluctuations of the loop regions. A good match is observed with experimental small angle X-ray scattering (SAXS) and NMR observables, such as chemical shifts and [Formula: see text] -coupling, with the best match obtained for the chemical shifts. However, deviations are observed in the water dynamics and protein-water interactions which we attribute to the limitation of solvent screening in the coarse-grain force field. The computational speed-up achieved is about 2-3 times compared to an all-atom system. Overall, the hybrid model is able to retain the main features of the underlying atomistic conformational landscape with a two-fold speed-up in computational cost.