Structure Characteristics Studies On Fully Disordered And Semi-disordered Areas Of Homologous Intrinsically Disordered Proteins By The Computer Simulations

The intrinsically disordered protein does not form a stable three-dimensionalstructure under physiological condition. They keep dynamic in various unstableconformations. This kind of structural characteristics of intrinsically disordered proteinsrelies on the characteristics of sequences. The structural characteristics also influencefunctional characteristics of intrinsically disordered proteins. The energy potential map ofan ordered protein forms funnel-shaped shape. The energy potential map of anintrinsically disordered protein forms zigzag shape. There are many potential minimaclosing to the similar value. Intrinsically disordered proteins may converse dynamicallybetween these potential minima. Structure flexibility and structural conversion ofelasticity of intrinsically disordered proteins play beneficial effects on functionrealization. These effects are different from ordered proteins. Sequence, structural andfunctional characteristic information of intrinsically disordered proteins are differentfrom ordered proteins. Those characteristic information remain to be further mining.Flagellum is the movement organ of bacteria. The moving speed and directionregulation of bacteria are dependent on the structure adjustment of the flagellum. FlgMprotein is the negative regular protein of flagellar formation. FlgM protein can control thegrowth and the length of the flagellum. FlgM protein is the key protein of flagellarmovement. Homologous FlgM proteins are treated as a kind of typical intrinsicallydisordered proteins. They have different disordered degrees, including fully disorderedstate and semi-disordered state. The research on homogenous FlgM proteins can helpmine more disordered and ordered characteristics. These characteristics providecharacteristic parameters for the prediction of intrinsically disordered proteins. The two sorts of FlgM proteins from the thermophiles aquifex aeolicus andSalmonella typhimurium are typical FlgM proteins, most studied. We used the two FlgMproteins as the research objects. The unfolded FlgM protein from the thermophilesaquifex aeolicus is called semi-disordered region on the N-terminal and ordered regionon the C-terminal. When it combines, the C-terminal forms ordered structure and theN-terminal forms orderly helical structure. The unfolded FlgM protein from salmonellatyphimurium is called fully disordered region on the N-terminal and ordered region onthe C-terminal. When it combines, the C-terminal forms ordered structure and theN-terminal maintains disordered structure. The disordered state of the two FlgM proteinsis the main reason that we selected them as the research object.Molecular dynamics simulation is an important mean of study on protein structuralcharacteristics. Study on the process of the flexibly structural conversion of intrinsicallydisordered proteins is an important aspect of exploration of structural and functionalcharacteristics of intrinsically disordered proteins. For instable intrinsically disorderedproteins, it is the limit of experiment method that makes it hard to get definite anddistinct structure characteristics. Compared with the experiment method, moleculardynamics simulation can get the specific protein conformational ensemble, and theinformation about structure and potential energy by a variety of analysis tools. We usedthe molecular dynamics simulation as a research method in this paper. We studied theinfluence of temperature on two FlgM proteins from the thermophiles aquifex aeolicusand Salmonella typhimurium and analyzed structure characteristics of the differentdisorder structures.The first part of this paper firstly introduces the intrinsically disordered protein,flagella and FlgM protein, temperature and homologous FlgM proteins and the analysisof two homologous FlgM proteins on sequences, experiments and disordered states. Thesecond part introduces the principle and application of molecular dynamics simulation.The third part is the study of two different temperatures on FlgM protein from thethermophiles aquifex aeolicus using molecular dynamics simulation. The result showsthat the difference in physiological temperature is one of the important parameters thataffect structure formation of the intrinsically disordered protein. The fourth part is the study on FlgM proteins from the thermophiles aquifex aeolicus and Salmonellatyphimurium using molecular dynamics simulation. The result shows that there aredifferences in structure characteristics in respect of conformation looseness, secondarystructure and tertiary structure between the fully disordered state, semi-disordered stateand ordered state. The fifth part is the conclusion and prospects of these works in thispaper.