The Study Of Protein Folding Theory

The main content of this thesis is employed replica exchange molecular dynamics (REMD) to study the folding process of protein and peptide. Protein folding process is constructed by the dynamics process which is the unfolding state of the protein to the folding state of the protein. This process can enable us to understand the amino acid sequence is how to determine protein structure and predict the thermodynamic and kinetic properties which is shown in the structure. At the same time, the protein misfolding also can lead to the occurrence of a number of deadly diseases, such as the prion diseases is caused by protein misfolding. The above problems are very meaningful and it can help us to better understand protein folding.Currently, there are mainly two aspects of research which are the structure and function of protein and the studying method is molecular dynamics simulation (MD). This method allows for detailed examination of the complex internal motions and conformational changes in proteins, which if often important for understanding protein function. Furthermore, MD simulations provide uniquely detailed information necessary to understand protein folding and, crucially, disease-related protein folding, such as prion diseases which we can use MD to study the misfolding mechanism of prion protein. Accurate all-atom MD simulations have been performed on studying the structure and function of protein. The basic principle of MD is applied force field which described intra-molecular and inter-molecular interactions. And calculate the protein trajectories in the phase space according to Newtonian mechanics and get the required macroscopic physical quantities. For the accuracy of molecular dynamics simulation is based two aspects:Firstly, the accuracy of the force field which contains many parameters. These parameters mainly are included the atom charge, interaction potential between the atoms. When two atoms close to each other, the polarization will make their charge redistribution. However, under standard nonpolarizable force field such as AMBER03, the atomic charges are fixed and therefore no polarization effect is included in the dynamics simulation. There currently exist a number of polarizable models for proteins for MD simulation, such as Jay L.Bank and co-workers developed fluctuating point charge model. But these models at present are still too complicated to apply and their accuracy still needs to be further validated. Here we propose a simple polarization model specifically for hydrogen bond-backbone hydrogen bonding (PHB model) and get some results. Secondly, the simulation time length and simulation scale size. In order to reduce the finite size effects, the researchers perform the periodic boundary conditions and for the time effects, we need the high computational efficiency computer. Of course, we need new simulation method to improve the computational efficiency. Replica exchange molecular dynamics is mostly applied to the protein folding, which has high computational efficiency compared to the traditional molecular dynamics simulation. In the international arena, development of new folding method and force field are the major aspects for protein folding in order to optimize the original force field and achieve a precise description of molecular simulation.This thesis contains mainly three parts:Part I:Polarization of intra protein hydrogen bond is important to thermal stability of short helix; Part Ⅱ:The intrinsic helical propensities of the helical fragments in the prion protein under neutral and low pH conditions:A replica exchange dynamics study; Part Ⅲ:The shortcomings of this thesis and studying direction in the future;Ⅰ Polarization of intra protein hydrogen bond is critical to thermal stability of short helixSimulation result for protein folding/unfolding is highly dependent on the accuracy of the force field employed. Even for the simplest structure of protein such as a short helix, simulations using the existing force fields often fail to produce the correct structural/thermodynamic properties of the protein. Recent research indicated that lack of polarization is at least partially responsible for the failure to successfully fold a short helix. In this work, we develop a simple formula-based atomic charge polarization model (PHB model) for intra-protein (backbone) hydrogen bonding based on the existing AMBER force field to study the thermal stability of a short helix (2I9M) by replica exchange molecular dynamics simulation. By varying the donor-acceptor distance but keeping the other geometries of the dialanine fixed, we obtained RESP charges for the donors and acceptors at discrete points along the bond length (shown as the dashed line in Fig. La) between2.5A to6.5A. The calculated amount of charge deviations from their asymptotic values for atoms N and O are shown in Fig.l (red diamonds), both of which can be fitted to a single-exponential function (blue curves). In this approach, no charge transfer between residues is allowed and only the atomic charges of the N, H, C and O atoms in the hydrogen bond are varied. Thus, the amount of transferred charge for H and C atoms is exactly the negative of that for N and O atoms, respectively. The fitted functional forms are ΔqN=-6.228×exp(-0.455×R) ΔqH=6.228×exp(-0.455×R) AndΔqO=-1.847×exp(-0.466×R) ΔqC=1.847×exp(-0.466×R)By comparing the simulation results with those obtained by employing the standard AMBER03force field, the formula-based atomic charge polarization model gave the helix melting curve in close agreement with the NMR experiment. However, in simulation using the standard AMBER force field, the helix was thermally unstable at the temperature of NMR experiment, with a melting temperature almost below freezing point. The difference in observed thermal stability from these two simulations is the effect of backbone intra-protein polarization which was included in the formula-based atomic charge polarization model. The polarization of backbone hydrogen bonding thus plays a critical role in the thermal stability of helix or more general protein structures.Part Ⅱ:The intrinsic helical propensities of the helical fragments in the prion protein under neutral and low pH conditions:A replica exchange dynamics studyTransmissible spongiform encephalopathies(TSE) is a series of fatal neurodegenerative diseases that occur in many species such scrapie in sheep, chronic wasting disease in deer and Creutzfeldt-Jakob disease (CJD), Kuru in humans. TSE have been attributed to the structural conversion of prion. The normal, cellular form of PrP (PrPc) is not pathogenic, but PrPc can transform the abnormal and infectious Scrapie isoform of PrP (PrPSc) under certain conditions, then which can cause the TSE diseases. Although PrPc and PrPSc have the same residue sequences, but have the large differences in their conformations. PrPc was soluble, rich in a-helix, while PrP Sc was not soluble, rich in (3structure and can form the insoluble amyloid. So far, the conformation change of prion diseases is still a mystery. As the PrPC was rich in ahelix and PrPSc had many βstructure, which give rise to the hypothesis that the ahelix of prion maybe transform β structure. So Replica exchange molecular dynamics simulations in neutral and acidic aqueous solutions have been employed to study the intrinsic helical propensities of three helices in both Syrian hamster (syPrP) and human (huPrP) prion proteins. The helical propensities of syPrP HA and huPrP HA are very high under both pH conditions, which infers that HA is hardly involved in the helix to β transition. SyPrP HB chain has strong tendency in extended conformation, which is possibly responsible for the infection of prion disease for Syrian hamster. HuPrP HC has larger preference for the extended conformation than huPrP HA and huPrP HB do, which leads to the conjecture that it is more likely the participator of β rich structure for human prion protein. We also noticed that the occurrence of salt bridges shows no correlation with the helical propensity, indicating that salt bridge is not a stabilizer of helix.Part Ⅲ:Prospects and OutlookIn the first part, we proposed a formula-based polarizable hydrogen bond model (PHB model) that can be implemented in REMD simulation which has been applied to studying the folding and the thermal stability of a short helical peptide2I9M. The melting temperature is about286K (just above the NMR experimental temperature273K) and the folding is a direct downhill folding. We believe that this PHB model is a promising method for computational study of proteins or other biopolymers. For second part, we just study the three a-helix fragments independently by REMD and do not consider the effect of the interaction between them for the conformation changes; At the same time, we used the GB solvation model and the simulation time is not enough, which can explain why we can’t see the large conformational change. Thus we will employ the coarse-grained molecular dynamics to study the long time dynamics for the whole prion protein with the explicit water;...