The Development And Application Of Polarized Protein-Specific Charge And Molecular Dynamics Simulations Of Macromolecular

Molecular dynamics (MD) simulation is one of the popular tools to study all kinds of properties of biological macromolecules, such as:predicting the binding affinity between proteins and ligands, studying the mechanism of protein folding、the interactions between proteins and membrane、the mechanism of ion channels and the catalytic reactions of enzyme, etc. Then the technology of MD simulations gradually grasp the attention of scientists. The main idea of MD simulation is based on a mathematical model of a molecule as a collection of balls corresponding to the atoms, the springs are used to connect atoms. The movement of molecules is based on the high-dimensional potential energy surface. At present, there are various potential energy functions, such as:AMBER, Charmm, opls and so on. All these potential energy functions are composed of two parts:bonded interactional energy and non-bonded interactional energy. Bonded interactional energy includes:bond stretch, angle bending, dihedral terms, non-bonded interactional energy includes:Electrostatic and Van der waals (VDW) interactions. The different parameters of potential energy contribute to different force fields. Electrostatic interactions is long-range interactional force and play an important role during MD simulations. The fallacious description of hydrogen bond and salt bridge interactions are main due to the incorrect of electrostatic interactions. While there are much results can prove that the hydrogen bond and salt bridge interactions are very important for studying the mechanism of protein folding and interactions between protein and ligand, etc. The molecular mechanics (MM) calculated the electrostatic interactions based on the theory of coulomb and every atom carries point charge centered on the atom. The point charge is fitted the electric potential around molecules. Classic force fields view point charge as an unchanged value which will not affected by surrounding environment. In fact, the biological macromolecules are surrounded by waters. Water molecules are polar molecules that can polarize the macromolecules, the polarized macromolecules also can polarize the water molecules, then cause the redistribution of charge. So we must consider the effect of polarization between macromolecules and solvent.Now there are various models can include polarization, such as:Drude oscillator, fluctuating charge model and induced dipoles model. But there are still some inevitable defects:Drude oscillator introduce a fictitious particle connecting with every atom, induced dipoles model costs too much computation times, so the combination between induced dipoles model and MD simulation is not reality, the transformation of force field also is very hard to be reached. Our group completely discard the transformation of force field and develop a method to consider the polarization of environment. With the help of molecular fragmentation with conjugate caps method, we can divide the protein into based-residue fragment, then the electric potential of each fragment is calculated with quantum mechanics and the effect of environment is include as the background charge, at last the protein-specific polarized charge (PPC) is fitted.The PPC of buried atoms fitted with RESP method have large fluctuation along with the change of conformations. The large fluctuation will do harm to MD simulations. Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges, we have proposed a numerically stable restrained electrostatic potential (ESP)-based charge fitting method for protein:dRESP. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER, Charmm, OPLS charge), and the residual part is to be determined by restrained fitting to residual ESP on grid points around the molecule. Nonuniform weighting factors as a function of the dominant charge are assigned to the atoms. Because the residual part is several folds to several orders smaller than the dominant part, the impact of ill-conditioning is alleviated. The results testify that the fluctuation can be decreased regardless of the predefined charge, so the method avoid the numerical problems.The binding affinity between streptavidin and biotin is-18.1kcal/mol which is the largest binding affinity found in nature. This complex is invaluable for rational drug design. A large number of research results testify that the network of hydrogen bond between streptavidin and biotin (BTN) is main force driving BTN binding to streptavidin. Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a4.2kcal/mol reduction in biotin binding affinity, the RMSD value calculating through superimposing the A subunits of the wild type (WT) and mutant (F1301) structure using Ca atoms of the subunit cores is0.377A. We carry out molecular dynamics simulations with AMBER and polarized dRESP charge, then apply MM/PBSA method to calculate the binding free energies of biotin to WT and F130L. The absolute binding affinities based on AMBER charge are repulsive, and the mutation induced binding loss is underestimated. When using the polarized protein-specific charge, the absolute binding affinities are significantly enhanced. In particular both the absolute and relative binding affinities are in line with the experimental measurements. This work verifies Baugh’s conjecture that electrostatic polarization effect plays an essential role in modulating the binding affinity of biotin to the streptavidin through F130L mutation。Cytochrome P450(CYP) is a large group of enzymes that catalyze the oxidation of bound substances. It will involve the phase I metabolism of70-80%drug, so may play a key role between drug and drug interaction. CYP2J2mainly expressed in extrahepatic tissues, including intestine and cardiovascular systems is a subfamily of CYP enzyme. There are a lot of researches can proved that CYPJ22can metabolize a wide range of structurally diverse drugs and play an indispensable role in first-pass metabolism and drug-drug interactions, but the general role of CYP2J2in drug metabolism is not yet fully understood. Molecular docking is main tools for computer-aided drug design, we apply the technology of experiment、molecular docking and MD simulations to screened69know marketed drugs for inhibition of CYP2J2. We discovered two drugs as potent and selective CYP2J2inhibitors:telmisartan and flunarizine. They have CYP2J2inhibition IC50values of0.42mM and0.94mM, respectively, which are at least10-fold more selective against all other major metabolizing CYPs; moreover, they are not substrates of CYP2J2. So telmisartan and flunarizine are ideal tools for study the metabolic mechanism of CYP2J2. Molecular docking and MD simulation consolidate the results of experiments. The detailed structures information of conformations unveil that telmisartan is non-competitive inhibitor, while flunarizine compete with substrate for same binding site.