Contraction Of M5G Molecular Modeling Platform And Studies On The Protein Analog Solution

Related studies on Protein are the focus of the post-genome era. Maintaining the three-dimensional structure of proteins is the physical basis for the exercise of all specific biological function of proteins. Research of protein folding becomes the core subject related to protein design and molecular biology. Model compounds to proteins and protein molecular model are used to study the thermodynamic driving force of protein folding and solvention of protein. The theoretical and experimental methods (molecular simulation and microcalorimetry), which are widely used in protein folding research, are discussed.There is a "microsecond barrier" in all-atoms molecular dynamics simulation of protein folding. Computer simulation of protein folding integrates motion equation in fetosecond stepwidth, and the real protein folding process takes milliseconds to seconds. Using virtual execution environment and mobile agent technologies, M5G, a P2P public resource computation platform was constructed. M5G harvests idled PCs' CPU cycles, uses these computational resource in coarse-grained parallel molecular dynamics computer simulation.The microcalorimetry is a very important tool for researches of protein. It can provide much thermodynamic information about the interactions between protein molecule and the solvent (or denaturator) molecules. A flow-mixing isothermal microcalorimeter was constructed, tested, calibrated and used to measure the excess enthalpies of some industrial solvents.The microcalorimeter was used to study the thermodynmics behavior of protein anology solutions. Amide, as a simple model compound of protein molecules, was studied. Three alcohols were used as a model to study the polyhydroxy compounds in water molecules interact with proteins. The enthalpies of amide in a diluted solution of alcohols were measured. The solute-solute and solute-solvent interactions of these solutions are discussed according to McMillan-Mayer's theory.Molecular modeling and computer simulation are the basic tools to study protein folding. Most simplified models of protein don't explicitly consider solvent effects. It can not be used to compare the contribution of diffent solvents. A new explicit solvent modified model was introduced into the modeling of solvention of protein, and was used in the computer simulation of protein folding.The opposite roles of TMAO and urea solution on the protein folding were studied through the all atoms molecular dynamics simulations. After comparative analyze of the solution structure, molecular structure and charge distribution of the solvent, the results of simulations give us the intrinsic difference between TMAO and urea aqueous solution.Based on M5G platform, Parallel replication exchange method was used in the all atom molecular dynamics simulations of a 15-residues peptide analogy. These simulations were accelerated by parallel distributed computation. Linear speedup was achieved on the 10M-network-connected personal computers,α-Helix-forming events were captured, and structure and dynamics properties of peptide solutions were obtained.