Molecular Dynamics On The Interaction Of Biological Systems

Structure determines function; function depends on the dynamic structure of the material. Above thelevel of the molecules and supramolecular aggregates ordered and higher-order structure, mainly byhydrogen bonding, salt bridges, some weak covalent bond and interactions and van der Waals makemolecules together. The interaction networks between these weak interactions are the foundation for thestable organisms themselves and related system spatial structure and biological functions. For example:Protein is the main component of cells, the important physiological activities in vivo are accomplished by theprotein. The interaction of protein itself and protein-protein plays important role in many fields, such as thecopy of genetic material, the expression of gene regulation, cell metabolism, and cell signal transduction, theshort-range and long-range communications between cells and cells, organism morphogenesis, cell adhesion.Crystal growth and morphology changes play a vital role to the nature of the crystal itself. Research showsthat even small amounts of impurities and additives will bring about larger crystal morphology effects. Inorder to obtain crystals of different morphologies to exert their desired function, in some cases, to add anadditive intended to crystal growth and changes in morphology control, especially the study ofbiocompatibility materials to development and application of implant materials in vivo are very significant,so understanding the interaction mechanism between additives and crystal will help us understand the tworoles in molecular scale, and this was improved and molecular design. In order to study the interactionbetween network conditions such processes on the atomic scale, computer molecular modeling has shown astrong advantage, become a powerful tool in addition to experimental research tools. In this work, the salt bridge interaction network and stability of mammalian prion proteins in water werestudied by molecular dynamics (MD) and flow molecular dynamics (FMD) simulation. Tn this basis,molecular mechanism was used to study the interaction network between insulin-like growth factor (IGF)and IGF binding proteins (IGFBPs) by MD. Finally, quantum mechanism was used to build the Force fieldfile of the polyvinylpyrrolidone (PVP), and then we investigated the interaction network betweenhydroxyapatite (HAP) and polyvinylpyrrolidone (PVP). In this way, the key interaction network and theinteraction mode could be found between protein and different kinds of interfaces, such as itself, protein,inorganic crystal materials and so on. And those findings could be applied in the fields of drug design,biomedical materials. The major contributions of this work are as follows：1. Study on salt bridge interaction network and stability of mammalian prion proteins by MD and FMD.The salt bridge network of the two proteins was mapped. And we analyzed the relationship between stabilityand molecular interaction of mammalian prion proteins in balance and disturbed states. It was found thatmost key salt bridges with persistent occupancy were found to link the rigid helix and the flexible loop tokeep the contact between the two different secondary structures elements. Moreover, the intra-helix saltbridges were associated with backbone H-bonds, and the two interactions worked together to stabilize thehelix.Moreover, the intra-helix and inter-helix salt bridge can help to stabilize the α-helix.2. Molecular dynamics study on interaction network between insulin-like growth factor bindingProtein-2(IGFBP2) and insulin-like growth factor (IGFs). The IGFs molecules as a probe molecule, thebinding sites between IGF1, IGF2and C-BP-2were scanning search in72systems, and drawed theinteractions distribution of surface residue between IGFs and C-BP-2. The key residues were classified andprobability statistics and we studied the interaction mechanism of those systems by types of action, change ofdistance, interaction energy and so on. 3. Molecular simulation study of the effect of polyvinylpyrrolidone (PVP) on hydroxyapatite (HAP)Crystal Habit. We studied the interaction between three kinds of aggregation states of PVP and the surfaceof HAP (002) and between one aggregation states of PVP and surfaces of HAP (002),(001),(010). In theformer, as the PVP was flexible, it can conclude that the adsorption process exists in the larger structureadjustment of PVP as well as the interaction between PVP and the HAP. These two kinds of competition arethe main cause to the differences in the interaction between PVP and HAP and the order of the interactionenergy was：（c）>（b）>(a). Moreover, the interaction energy between aggregation states of (b) on the surfaceHAP (001)(010)(002) was: HAP (001)> HAP (010)> HAP (002). We studied the interaction between PVPand HAP by through studied the effect of the aggregation state of PVP molecules and molecular orientation,HAP crystal surface structure, surface charge distribution and other factors. Further, the analysis ofinteraction energy, contact area, RMSF, adsorption driving force, distance revealed the mechanism ofinteraction between the PVP and HAP, and we compared with experimental results. Our results elucidatedthe interaction mechanism between the additives and crystal in the molecular level, we also provides thetheoretical basis for control crystal morphology and molecular design.