Martini 3 coarse-grained force field for poly(para-phenylene ethynylene)s

O-glycans Expand Lubricin and Attenuate Its Viscosity and Shear Thinning

Lubricin, an intrinsically disordered glycoprotein, plays a pivotal role in facilitating smooth movement and ensuring the enduring functionality of synovial joints. The central domain of this protein serves as a source of this excellent lubrication and is characterized by its highly glycosylated, negatively charged, and disordered structure. However, the influence of O-glycans on the viscosity of lubricin remains unclear. In this study, we employ molecular dynamics simulations in the absence and presence of shear, along with continuum simulations, to elucidate the intricate interplay between O-glycans and lubricin and the impact of O-glycans on lubricin's conformational properties and viscosity. We found the presence of O-glycans to induce a more extended conformation in fragments of the disordered region of lubricin. These O-glycans contribute to a reduction in solution viscosity but at the same time weaken shear thinning at high shear rates, compared to nonglycosylated systems with the same density. This effect is attributed to the steric and electrostatic repulsion between the fragments, which prevents their conglomeration and structuring. Our computational study yields a mechanistic mechanism underlying previous experimental observations of lubricin and paves the way to a more rational understanding of its function in the synovial fluid.

Electronic spectra of jet-cooled 1,4-bis(phenylethynyl)benzene: Strength in π-electron conjugation and two large-amplitude torsional motions

To spectroscopically qualify strength in the π-electron conjugation, the electronic spectra of jet-cooled 1,4-bis(phenylethynyl)benzene (BPEB) in the region of the transition to the lowest excited singlet (S1) 1B1u state are measured by the fluorescence excitation and the single-vibronic-level dispersed fluorescence methods. Strength is defined as the difference in potential energies between the planar and perpendicular conformations. BPEB possesses two large-amplitude torsional motions, out-of-phase 24 and in-phase 29 modes. The most stable is the planar conformation, and barrier heights at the perpendicular conformation are coincident in torsional potentials for the two modes. Torsional levels are successively observed up to 19± and 16- quantum levels in the ground state, respectively. Strength is determined to be 293 cm-1 (3.51 kJmol-1) with an accuracy of an error range smaller than 1 cm-1. In the excited state, strength is estimated to be 1549 ± 73 cm-1. Combination levels of two torsional modes are also measured up to high quantum levels. A systematic decrease in frequencies is observed with increasing the quantum number. Quantum-chemistry calculations of B3LYP, CAM-B3PLYP, WB97XD, and M062X with basis sets of aug-cc-pVDZ are performed, where B3LYP theories are carried out with the dispersion correlation. The calculated strength is 1.1-2.1 times larger than observed.

Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications

Protein lipidations are vital co/post-translational modifications that tether lipid tails to specific protein amino acids, allowing them to anchor to biological membranes, switch their subcellular localization, and modulate association with other proteins. Such lipidations are thus crucial for multiple biological processes including signal transduction, protein trafficking, and membrane localization and are implicated in various diseases as well. Examples of lipid-anchored proteins include the Ras family of proteins that undergo farnesylation; actin and gelsolin that are myristoylated; phospholipase D that is palmitoylated; glycosylphosphatidylinositol-anchored proteins; and others. Here, we develop parameters for cysteine-targeting farnesylation, geranylgeranylation, and palmitoylation, as well as glycine-targeting myristoylation for the latest version of the Martini 3 coarse-grained force field. The parameters are developed using the CHARMM36m all-atom force field parameters as reference. The behavior of the coarse-grained models is consistent with that of the all-atom force field for all lipidations and reproduces key dynamical and structural features of lipid-anchored peptides, such as the solvent-accessible surface area, bilayer penetration depth, and representative conformations of the anchors. The parameters are also validated in simulations of the lipid-anchored peripheral membrane proteins Rheb and Arf1, after comparison with independent all-atom simulations. The parameters, along with mapping schemes for the popular martinize2 tool, are available for download at 10.5281/zenodo.7849262 and also as supporting information.

Approaches and Perspective of Coarse-Grained Modeling and Simulation for Polymer-Nanoparticle Hybrid Systems

Molecular modeling and simulations have emerged as effective and indispensable tools to characterize polymeric systems. They provide fundamental and essential insights to design a product of the required properties and to improve the understanding of a phenomenon at the molecular level for a particular system. The polymer-nanoparticle hybrids are materials with outstanding properties and correspondingly large applications whose study has benefited from this new paradigm. However, despite the significant expansion of modern day computational powers, investigation of the long time and large length scale phenomenon in polymeric and polymer-nanoparticle systems is still a challenging task to complete through all-atom molecular dynamics (AA-MD) simulations. To circumvent this problem, a variety of coarse-grained (CG) models have been proposed, ranging from the generic CG models for qualitative properties predictions to more realistic chemically specific CG models for quantitative properties predictions. These CG models have already delivered some success stories in the study of several spatial and temporal evolutions of many processes. Some of these studies were beyond the feasibility of traditional atomistic resolution models due to either the size or the time constraints. This review captures the different types of popular CG approaches that are utilized in the investigation of the microscopic behavior of polymer-nanoparticle hybrid systems. The rationale of this article is to furnish an overview of the popular CG approaches and their applications, to review several important and most recent developments, and to delineate the perspectives on future directions in the field.