Self-Assembly Mechanism Of Transmembrane Protein

As the main bearer of the membrane, membrane proteins play an important role in drug targeted therapy. In this essay, we make use of the Coarse-Grained molecular dynamic simulation and biological molecular experience to study the molecular mechanism of two transmembrane protein--RAGE and C99, which are respectively involved in diabetes and Alzheimer diseases.Existing literatures suggest that the dimerization of transmembrane domain drive the self-assembly of RAGE. We carried out mutation of the specific amino acid in the transmembrane domain of the RAGE and simulated various sequence of RAGE to find out whether the amino acid or the domain works in the dimerization, which is important to understand the assembly mechanism. In our results, we find that G6XXG9XXG12 motif in TM domain drive the recognition of dimerization, and PR and CYTO domains keep the conformation stable.As regarded to C99, we respectively simulated two C99 monomers in POPC/POPG(3:1) membrane, and one monomer or two C99 monomers in POPC/POPG/CHOL(3:1:1) membrane. Under multiple conditions, C99 monomers form a stable dimer which is predominantly right-handed coiled-coil. We find that the amino acid contact of packing interface are that MET21-VAL22, VAL25-VAL26, THR29-VAL30.Secondly, the C-terminal and N-terminal of C99 TMD both have weak interactions with cholesterols, forming unstable combinations, rather than 1:1 strong binding. The residues in association with cholesterol of c99 are also identified as below:GnXXXG15XXXG19, GLY24, ALA28, ILE31, VAL32, ILE33, LEU35, VAL36, above all are aliphatic amino acid. From the protein-restraint CG simulation, we put forward a multi-sites cholesterol binding model based on an equilibrated C99 conformation (2LLM PDB structure). It might be plausible that, the essence of the association between cholesterol and C99 is binding the cholesterol head by hydrogen bonding and binding the cholesterol body by appropriate structural domain consisting of the neutral aliphatic amino acids (AGLIV). Such binding model, in which the backbones of G24xxxA28 motif are completely exposed without cholesterol converging shelter, might help y-secretase identify the cleavage sites and then promote y-cleavage.Finally, there is no competition between C99 homo-dimerization and the cholesterol binding, it is clear that the contact residues of C99 in dimerization are totally different with those in the association with cholesterol, thus, the dimerization of C99 and association with cholesterol don’t disrupt each other. Our results provide a detailed picture of cholesterol binding and the theoretical foundation for studying potential influence of cholesterol on the C99 dimerization and on the processing of y-cleavage.Because of the complex mechanism of membrane protein, the traditional molecular simulation is difficult to deeply study the micro process. The atom model (atomistic model) can only calculate sub-microsecond range of molecular dynamic process due to consideration of the various details of atomic, while the general molecular process of cells always need ns-s time. Thus, in this article, we mainly adopt the coarse-grained simulations to improve the feasibility of computational simulation. Compared with the atomistic model, it is less amount of calculation, and more convenient.