相关论文: An Allosteric Model for the Influence of $\text{H}…
Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present…
Abnormal hemoglobins can have major consequences for tissue delivery of oxygen. Correct diagnosis of hemoglobinopathies with altered oxygen affinity requires a determination of hemoglobin oxygen dissociation curve (ODC), which relates the…
Modeling of polymer oxidative aging has been actively studied since the 1990s. Insights from these studies suggest that the transport of oxygen and radicals significantly influences aging heterogeneity, alongside chemical reaction kinetics.…
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed…
In this article we use all-atom simulations to elucidate the mechanisms underlying conformational switching and allostery within the coat protein of the bacteriophage MS2. Assembly of most icosahedral virus capsids requires that the capsid…
In GO/MoSe2 semiconductor heterostructure, we have demonstrated a subtle control on the doping dynamics by modulating interlayer coupling through the combination of strain-reducing relative rotation of the constituting layers and variation…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
Coulomb repulsion between the unevenly-bounded bonding "-" and nonbonding ":" electron pairs in the "O2- : H+/p-O2-" hydrogen-bond is found to originate the anomalies of low-compressibility, phonon relaxation dynamics, proton symmetrization…
We investigate the role of carbon monoxide ice in the chemical evolution of prestellar cores using astrochemical rate equation models. We constrain the ratios of the binding energies on CO ice and H$_{2}$O ice for a series of adsorbates…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
A basic model of hydrogen bonds related to $\rm{H}_2\rm{O}$, which is adapted from the Jaynes--Cummings model, is suggested, and its different dynamic features are studied theoretically. In this model, the making and breaking of hydrogen…
Carbon monoxide (CO) and nitrous oxide (N2O) both undergo profound structural and chemical transformations when compressed. While their individual high-P/T phase diagrams have been mapped in considerable detail, comparatively little…
We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior;…
The original ideas of Cooper and Dryden, that allosteric signalling can be induced between distant binding sites on proteins without any change in mean structural conformation, has proved to be a remarkably prescient insight into the rich…
Allosteric signaling in biological molecules, which may be viewed as specific action at a distance due to localized perturbation upon binding of ligands or changes in environmental cues, is pervasive in biology. Phenomenological MWC and KNF…
We develop a model of molecular binding based on the Bohr-Sommerfeld description of atoms together with a constraint taken from conventional quantum mechanics. The model can describe the binding energy curves of H2, H3 and other molecules…
A growing number of experimental evidence shows that it is general for a ligand binding protein to have a potential for allosteric regulation and for further evolution. In addition, such proteins generically change their conformation upon…
In allosteric proteins, binding a ligand can affect function at a distant location, for example by changing the binding affinity of a substrate at the active site. The induced fit and population shift models, which differ by the assumed…
We study the effects of H2O on CO2 adsorption in an amine-appended variant of the metal-organic framework Mg2(dobpdc), which is known to exhibit chaining behavior that presents in a step-shaped adsorption isotherm. We first show how the…
Recently experiments have shown very significant spin activity in biological molecules such as DNA, proteins, oligopeptides and aminoacids. Such molecules have in common their chiral structure, time reversal symmetry and the absence of…