binding energy

Based on different properties of structure of helical protein molecules some theories of bio-energy transport along the molecular chains have been proposed and established, where the energy is released by hydrolysis of adenosine triphosphate (ATP). A brief survey of past researches on different models and theories of bio-energy, including Davydov’s, Brown et al’s, Schweitzer’s, Cruzeiro-Hansson’s, Forner‘s and Pang’s models were first stated in this paper. Subsequently we studied and reviewed mainly and systematically the properties and stability of the carriers (solitons) transporting the bio-energy at physiological temperature 300K in Pang’s and Davydov’s theories. However, these theoretical models including Davydov’s and Pang’s model were all established based on a periodic and uniform proteins, which are different from practically biological proteins molecules. Therefore, it is very necessary to inspect and verify the validity of the theory of bio-energy transport in really biological protein molecules. These problems were extensively studied by a lot of researchers and using different methods in past thirty years, a considerable number of research results were obtained. I here reviewed the situations and progresses of study on this problem, in which we reviewed the correctness of the theory of bio-energy transport including Davydov’s and Pang’s model and its investigated progresses under influences of structure nonuniformity and disorder, side groups and imported impurities of protein chains as well as the thermal perturbation and damping of medium arising from the biological temperature of the systems. The structure nonuniformity arises from the disorder distribution of sequence of masses of amino acid residues and side groups and imported impurities, which results in the changes and fluctuations of the spring constant, dipole-dipole interaction, exciton-phonon coupling constant, diagonal disorder or ground state energy and chain-chain interaction among the molecular channels in the dynamic equations in different models. The influences of structure nonuniformity, side groups and imported impurities as well as the thermal perturbation and damping of medium on the bio-energy transport in the proteins with single chain and three chains were studied by differently numerical simulation technique and methods containing the average Hamiltonian way of thermal perturbation, fourth-order Runge-Kutta method, Monte Carlo method, quantum perturbed way and thermodynamic and statistical method, and so on. In this review the numerical simulation results of bio-energy transport in uniform protein molecules, the influence of structure nonuniformity on the bio-energy transport, the effects of temperature of systems on the bio-energy transport and the simultaneous effects of structure nonuniformity, damping and thermal perturbation of proteins on the bio-energy transport in a single chains and helical molecules were included and studied, respectively. The results obtained from these studies and reviews represent that Davydov’s soliton is really unstable, but Pang’s soliton is stable at physiologic temperature 300K and underinfluences of structure nonuniformity or disorder, side groups, imported impurities and damping of medium, which is consistent with analytic results. Thus we can still conclude that the soliton in Pang’s model is exactly a carrier of the bio-energy transport, Pang’s theory is appropriate to helical protein molecules.

The novel coronavirus 2019-nCoV has become a bane to mankind and spread worldwide and infected many people. Thus, there is an urgent need of a cure for the severe pneumonia disease caused by this virus. In this study, In silico comparative analysis has been done for HIV protease inhibitors on coronavirus 3CLpro protein which has shown the major interactions and common amino acid residues involved in interactions. The amino acid interaction analysis has revealed two amino acids ARG4, LYS5 to be the major amino acids targets among selected ligands. The binding energy analysis has also revealed Cobicistat as one of these best suited ligand for 3CLpro.

The emergence of Porphyromonas gingivalis biofilm is a hallmark of risky burden diseases including Alzheimer's disease and atherosclerosis. The current study aims to screen some natural essential oil compounds and coumarin derivatives to interfere with quorum sensing of the bacterium and thus biofilm formation. A total of 20 ligands (10 essential oil molecules and 10 coumarin derivatives) were docked to P.gingivalis  heme-binding protein HmuY using UCSF Chimera built-in AutoDock interface. Alongside, ADMET properties were also predicted via ADMETsar 2.0 and ProTox-II webservers. All of the selected ligands had higher free energy values than the reference inhibitor MES and native coumarin as well. Moreover, ADME parameters are in good agreement with Lipinski's rule of five. Nevertheless, the best molecules with top binding energy exhibited slight immunogenicity as well as carcinogenicity issues requiring in vitro confirmation. In conclusion, the tested ligands had better efficacy against P.gingivalis quorum sensing and biofilm.

An empirical framework that accurately describes radioactive binding energies is the Somewhat Empirical Mass Equation (SEMF). They showcase many implementations and uses of the idea that rely on graphics and printed objects. A key new addition is a contrast with real experiments, as well as a visualization of the energy environment as supplied by the SEMF. The shortcomings of the empirical theory are shown by our visualization of this differential energy scenery, which also highlights the significance of what is known as magic numbers—an explanation provided by the outermost approach, which was developed much more recently than the water drop theory. This provides a great chance to talk about the advantages and limitations of simulations everywhere within the framework of science teaching.