Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions.

Intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. One of the core problems is how do electrostatic repulsion and hydrophobic interactions in peptides regulate the phase separation process? To answer this question, this study uses random peptides composed of positively charged arginine (Arg, R) and hydrophobic isoleucine (Ile, I) as the model systems, and conduct large-scale simulations using all atom and coarse-grained model multi-scale simulation methods. In this article, we investigate the phase separation of different sequences using a coarse-grained model. It is found that the stronger the electrostatic repulsion in the system, the more extended the single-chain structure, and the more likely the system forms a low-density homogeneous phase. In contrast, the stronger the hydrophobic effect of the system, the more compact the single-chain structure, the easier phase separation, and the higher the critical temperature of phase separation. Overall, by taking the random polypeptides composed of two types of amino acid residues as model systems, this study discusses the relationship between the protein sequence and phase behaviour, and provides theoretical insights into the interactions within or between proteins. It is expected to provide essential physical information for the sequence design of functional IDPs, as well as data to support the diagnosis and treatment of the LLPS-associated diseases.

Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.

Riboswitches normally regulate gene expression through structural changes in response to the specific binding of cellular metabolites or metal ions. Taking add adenine riboswitch as an example, we explore the influences of metal ions (especially for K+ and Mg2+ ions) on the structure and dynamics of riboswitch aptamer (with and without ligand) by using molecular dynamic (MD) simulations. Our results show that a two-state transition marked by the structural deformation at the connection of J12 and P1 (CJ12-P1) is not only related to the binding of cognate ligands, but also strongly coupled with the change of metal ion environments. Moreover, the deformation of the structure at CJ12-P1 can be transmitted to P1 directly connected to the expression platform in multiple ways, which will affect the structure and stability of P1 to varying degrees, and finally change the regulation state of this riboswitch.

Rapid 3D roll-up of gas-phase planar gold clusters and affinity and alienation for Mg and Ge: A theoretical study of MgGeAun (n=1-12) clusters.

A cluster is a special matter level above a single atom and between macroscopic and microscopic matter, and it is an important bridge to understanding the relationship between the structure and function of matter. Here, we perform a comprehensive theoretical study of 2D planar Aun (n = 1-12) clusters doped with both magnesium and germanium. Two interesting results are found, namely the rapid 3D "roll-up" structural growth of the GeMgAun (n = 1-12) cluster ground state isomers, and the relative "alienation" of the different sizes of the Aun (n = 1-12) cluster framework towards the Ge atom, and the relative "affinity" towards the Mg atom. This study will not only enrich the data on gold-based clusters but will also provide a simple and clear theoretical guide for the 3D structuring of planar clusters, i.e. the doping of different classes of "affinition" and "alienatation" atoms.

Systematic research on gallium atom-doped neutral small- and medium-sized gas-phase magnesium clusters: A DFT study of GaMgn (n=2-12) clusters.

Structure, stability, charge transfer, chemical bonding, and spectroscopic properties of Ga atom-doped neutral Mgn (n = 2-12) clusters have been systematically investigated by CALYPSO and density functional theory. All cluster structures are based on "tetrahedral" and "yurt-like" growth except for GaMg2. The ground state isomer of GaMg8 with high symmetry structure is predicted to be the best-fit candidate for the "magic" cluster because of its excellent stability. Natural bond orbital calculations reveal that Ga and Mg atoms play the role of electron acceptor and donor in all ground state isomers, while the orbitals in both Ga and Mg are sp-hybridized. Most importantly, chemical bonding studies based on atom-in-molecular theory have shown that the lowest-energy state of GaMg4 is so special, in that it has not only the critical size for the appearance of Mg-Mg covalent bonds, but also the only cluster that has both Ga-Mg covalent and non-covalent bonds. Finally, theoretical calculations of IR and Raman spectra of all ground state isomers indicate that the spectra of these clusters are observable in the low-frequency band, and thus they can be identified by spectroscopic experiments. Furthermore, the bond heterogeneity of the Ga-Mg in the GaMg4 ground state isomer has also been specifically investigated, including the fixed GaMg4 structure with Mg atoms added in different directions, as well as ab initio molecular dynamics sampling at different temperatures.

Computational Exploration on the Structural and Optical Properties of Gold-Doped Alkaline-Earth Magnesium AuMgn (n = 2-12) Nanoclusters: DFT Study.

Using CALYPSO crystal search software, the structural growth mechanism, relative stability, charge transfer, chemical bonding and optical properties of AuMgn (n = 2-12) nanoclusters were extensively investigated based on DFT. The shape development uncovers two interesting properties of AuMgn nanoclusters contrasted with other doped Mg-based clusters, in particular, the planar design of AuMg3 and the highly symmetrical cage-like of AuMg9. The relative stability study shows that AuMg10 has the robust local stability, followed by AuMg9. In all nanoclusters, the charge is transferred from the Mg atoms to the Au atoms. Chemical bonding properties were confirmed by ELF analysis that Mg-Mg formed covalent bonds in nanoclusters larger than AuMg3. Static polarizability and hyperpolarizability calculations strongly suggest that AuMg9 nanocluster possesses interesting nonlinear optical properties. Boltzmann distribution weighted average IR and Raman spectroscopy studies at room temperature verify that these nanoclusters are identifiable by spectroscopic experiments. Finally, the average bond distance and average nearest neighbor distance were fully investigated.

Composition-related structural transition of random peptides: insight into the boundary between intrinsically disordered proteins and folded proteins.

Previous studies based on bioinformatics showed that there is a sharp distinction of structural features and residue composition between the intrinsically disordered proteins and the folded proteins. What induces such a composition-related structural transition? How do various kinds of interactions work in such processes? In this work, we investigate these problems based on a survey on peptides randomly composed of charged residues (including glutamic acids and lysines) and the residues with different hydrophobicity, such as alanines, glycines, or phenylalanines. Based on simulations using all-atom model and replica-exchange Monte Carlo method, a coil-globule transition is observed for each peptide. The corresponding transition temperature is found to be dependent on the contents of the hydrophobic and charged residues. For several cases, when the mean hydrophobicity is larger than a certain threshold, the transition temperature is higher than the room temperature, and vise versa. These thresholds of hydrophobicity and net charge are quantitatively consistent with the border line observed from the study of bioinformatics. These results outline the basic physical reasons for the compositional distinction between the intrinsically disordered proteins and the folded proteins. Furthermore, the contributions of various interactions to the structural variation of peptides are analyzed based on the contact statistics and the charge-pattern dependence of the gyration radii of the peptides. Our observations imply that the hydrophobicity contributes essentially to such composition-related transitions. Thus, we achieve a better understanding on composition-structure relation of the natural proteins and the underlying physics.

Neonatal Exposure to Low-Dose (1.2%) Sevoflurane Increases Rats' Hippocampal Neurogenesis and Synaptic Plasticity in Later Life.

The increasing usage of general anesthetics on young children and infants has drawn extensive attention to the effects of these drugs on cognitive function later in life. Recent animal studies have revealed improvement in hippocampus-dependent performance after lower concentrations of sevoflurane exposure. However, the long-term effects of low-dose sevoflurane on the developing brain remain elusive. On postnatal day (P) 7, rats were treated with 1.2% sevoflurane (1.2% sevo group), 2.4% sevoflurane (2.4% sevo group), and air control (C group) for 6 h. On P35-40, rats' hippocampus-dependent learning and memory was tested using the Morris water maze. Cognition-related and synapse-related proteins in the hippocampus were measured using Western blotting on P35. On the same day, neurogenesis and synapse ultrastructure were evaluated using immunofluorescence and transmission electron microscopy (TEM). On P35, the rats neonatally exposed to 1.2% sevoflurane showed better behavioral results than control rats, but not in the 2.4% sevo group. Exposure to 1.2% sevoflurane increased the number of 5'-bromo-2-deoxyuridine (BrdU)-positive cells in the dentate gyrus and improved both synaptic number and ultrastructure in the hippocampus. The expression levels of BDNF, TrkB, postsynaptic density (PSD)-95, and synaptophysin in the hippocampus were also increased in the 1.2% sevo group. In contrast, no significant changes in neurogenesis or synaptic plasticity were observed between the C group and the 2.4% sevo group on P35. These results showed that exposure of the developing brain to a low concentration of sevoflurane for 6 h could promote spatial learning and memory function, along with increased hippocampal neurogenesis and synaptic plasticity, in later life.