Muscarinic acetylcholine receptor-dependent and NMDA receptor-dependent LTP and LTD share the common AMPAR trafficking pathway

The forebrain cholinergic system promotes higher brain function in part by signaling through the M1 muscarinic acetylcholine receptor (mAChR). Long-term potentiation (LTP) and long-term depression (LTD) of excitatory synaptic transmis-sion in the hippocampus are also induced by mAChR. An AMPA receptor (AMPAR) trafficking model for hippocampal neurons has been proposed to simulate N-methyl-D-aspartate receptor (NMDAR)-dependent synaptic plasticity in the early phase. In this study, we demonstrated the validity of the hypothesis that the mAChR-dependent LTP/LTD shares a common AMPAR trafficking pathway associated with NMDAR-dependent LTP/LTD. However, unlike NMDAR, Ca2+ influx into the spine cytosol occurs owing to the Ca2+ stored inside the ER and is induced via the activation of inositol 1,4,5-trisphosphate (IP3) receptors during M1 mAChR activation. Moreover, the AMPAR trafficking model implies that alterations in LTP and LTD observed in Alzheimer's disease could be attributed to age-dependent reductions in AMPAR expression levels

Is F-1-ATPase a Rotary Motor with Nearly 100% Efficiency? Quantitative Analysis of Chemomechanical Coupling and Mechanical Slip

We present a chemomechanical network model of the rotary molecular motor F1-ATPase which quantitatively describes not only the rotary motor dynamics driven by ATP hydrolysis but also the ATP synthesis caused by forced reverse rotations. We observe a high reversibility of F1-ATPase, that is, the main cycle of ATP synthesis corresponds to the reversal of the main cycle in the hydrolysis-driven motor rotation. However, our quantitative analysis indicates that torque-induced mechanical slip without chemomechanical coupling occurs under high external torque and reduces the maximal efficiency of the free energy transduction to 40–80% below the optimal efficiency. Heat irreversibly dissipates not only through the viscous friction of the probe but also directly from the motor due to torque-induced mechanical slip. Such irreversible heat dissipation is a crucial limitation for achieving a 100% free-energy transduction efficiency with biological nanomachines because biomolecules are easily deformed by external torque

Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors

N-methyl-D-aspartate (NMDA) receptor-dependent long-term potentiation (LTP) and long-term depression (LTD) of signal transmission form neural circuits and thus are thought to underlie learning and memory. These mechanisms are mediated by AMPA receptor (AMPAR) trafficking in postsynaptic neurons. However, the regulatory mechanism of bidirectional plasticity at excitatory synapses remains unclear. We present a network model of AMPAR trafficking for adult hippocampal pyramidal neurons, which reproduces both LTP and LTD. We show that the induction of both LTP and LTD is regulated by the competition between exocytosis and endocytosis of AMPARs, which are mediated by the calcium-sensors synaptotagmin 1/7 (Syt1/7) and protein interacting with C-kinase 1 (PICK1), respectively. Our result indicates that recycling endosomes containing AMPAR are always ready for Syt1/7-dependent exocytosis of AMPAR at peri-synaptic/synaptic membranes. This is because molecular motor myosin V-b constitutively transports the recycling endosome toward the membrane in a Ca2+-independent manner

Immune response to SARS-CoV-2 in severe disease and long COVID-19

COVID-19 is mild to moderate in otherwise healthy individuals but may nonetheless cause life-threatening disease and/or a wide range of persistent symptoms. The general determinant of disease severity is age mainly because the immune response declines in aging patients. Here, we developed a mathematical model of the immune response to SARS-CoV-2 and revealed that typical age-related risk factors such as only a several 10% decrease in innate immune cell activity and inhibition of type-I interferon signaling by autoantibodies drastil ally increased the viral load. It was reported that the numbers of certain dendritic cell subsets remained less than half those in healthy donors even seven months after infection. Hence, the inflammatory response was ongoing. Our model predicted the persistent DC reduction and showed that certain patients with severe and even mild symptoms could not effectively eliminate the virus and could potentially develop long COVID

Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea

The origin of life is believed to be chemoautotrophic, deriving all biomass components from carbon dioxide, and all energy from inorganic redox couples in the environment. The reductive tricarboxylic acid cycle (rTCA) and the Wood-Ljungdahl pathway (WL) have been recognized as the most ancient carbon fixation pathways. The rTCA of the chemolithotrophic Thermosulfidibacter takaii, which was recently demonstrated to take place via an unexpected reverse reaction of citrate synthase, was reproduced using a kinetic network model, and a competition between reductive and oxidative fluxes on rTCA due to an acetyl coenzyme A (ACOA) influx upon acetate uptake was revealed. Avoiding ACOA direct influx into rTCA from WL is, therefore, raised as a kinetically necessary condition to maintain a complete rTCA. This hypothesis was confirmed for deep-branching bacteria and archaea, and explains the kinetic factors governing elementary processes in carbon metabolism evolution from the last universal common ancestor

Effects of hydrophobic hydration on polymer chains immersed in supercooled water

A multiscale simulation of a hydrophobic polymer chain immersed in water including the supercooled region is presented. Solvent effects on the polymer conformation were taken into account via liquid–state density functional theory in which a free-energy functional model was constructed using a density response function of bulk water, determined from a molecular dynamics (MD) simulation. This approach overcomes sampling problems in simulations of high-viscosity polymer solutions in the deeply supercooled region. Isobars determined from the MD simulations of 4000 water molecules suggest a liquid–liquid transition in the deeply supercooled region. The multiscale simulation reveals that a hydrophobic polymer chain exhibits swelling upon cooling along isobars below a hypothesized second critical pressure; no remarkable swelling is observed at higher pressures. These observations agree with the behavior of a polymer chain in a Jagla solvent model that qualitatively reproduces the thermodynamics and dynamics of liquid water. A theoretical analysis of the results obtained from the multiscale simulation show that a decrease in entropy due to the swelling arises from the formation of a tetrahedral hydrogen bond network in the hydration shell

Theoretical analysis on thermodynamic stability of chignolin

Understanding the dominant factor in thermodynamic stability of proteins remains an open challenge. Kauzmann's hydrophobic interaction hypothesis, which considers hydrophobic interactions between nonpolar groups as the dominant factor, has been widely accepted for about sixty years and attracted many scientists. The hypothesis, however, has not been verified or disproved because it is difficult, both theoretically and experimentally, to quantify the solvent effects on the free energy change in protein folding. Here, we developed a computational method for extracting the dominant factor behind thermodynamic stability of proteins and applied it to a small, designed protein, chignolin. The resulting free energy profile quantitatively agreed with the molecular dynamics simulations. Decomposition of the free energy profile indicated that intramolecular interactions predominantly stabilized collapsed conformations, whereas solvent-induced interactions, including hydrophobic ones, destabilized them. These results obtained for chignolin were consistent with the site-directed mutagenesis and calorimetry experiments for globular proteins with hydrophobic interior cores

Solvation free energies of alcohols in water: temperature and pressure dependences

Solvation free energies μ* of amphiphilic species, methanol and 1,2-hexanediol, are obtained as a function of temperature or pressure based on molecular dynamics simulations combined with efficient free-energy calculation methods. In general, μ* of an amphiphile can be divided into Image ID:d3cp03799a-t1.gif and Image ID:d3cp03799a-t2.gif, the nonpolar and electrostatic contributions, and the former is further divided into Image ID:d3cp03799a-t3.gif and Image ID:d3cp03799a-t4.gif which are the work of cavity formation process and the free energy change due to weak, attractive interactions between the solute molecule and surrounding solvent molecules. We demonstrate that μ* of the two amphiphilic solutes can be obtained accurately using a perturbation combining method, which relies on the exact expressions for Image ID:d3cp03799a-t5.gif and Image ID:d3cp03799a-t6.gif and requires no simulations of intermediate systems between the solute with strong, repulsive interactions and the solute with the van der Waals and electrostatic interactions. The decomposition of μ* gives us several physical insights including that μ* is an increasing function of T due to Image ID:d3cp03799a-t7.gif, that the contributions of hydrophilic groups to the temperature dependence of μ* are additive, and that the contribution of the van der Waals attraction to the solvation volume is greater than that of the electrostatic interactions

A solvation-free-energy functional: A reference-modified density functional formulation

The three-dimensional reference interaction site model (3D-RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation-free-energy (SFE) for large solute molecules in water. To improve the free-energy density functional for the SFE of solute molecules, we propose a reference-modified density functional theory (RMDFT) that is a general theoretical approach to construct the free-energy density functional systematically. In the RMDFT formulation, hard-sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction-site-model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side-chain analogues as well as for 504 small organic molecules