Structural Researches Of Two Epigenetic Modification Reading Proteins And Two Scaffolding Proteins In Human Body

Protein is one of the main biological molecules of the cell, whereas its structure is the molecular basis of its cell function. The reading proteins of epigenetic modification and scaffolding proteins are two important families, which function in membrane-associated molecular trafficking, signal transduction pathways, reading of post-translational modification and so on. The functions of the epigenetic modification reading proteins and scaffolding proteins have been researched adequately, and the structures of them have been reported, but the precise mechanisms of adaptor protein are still scanty. Hence, we resolved the crystal structures of four proteins of these protein families with X-ray crystallography, and analyzed the mechanisms of these proteins were with bioinformatics.Glycosylase domain of methyl-CpG(mCpG) binding domain Protein4(MBD4) and C2H2-type zinc finger of DPF2are two important proteins in epigenetic modification reading protein family. The crystal structure of glycosylase domain of MBD4shows that al, a8, a9and12-residue preceding al come together to form a hydrophobic core at the top of the cleft, while the residues in the hydrophobic core(Gln448, Tyr539, Asp559) are essential for the thymine recognition. The glycosylase domain of MBD4is involved in cross talking of different epigenetic modifications through its recognition of methylated DNA and its interacting ability with Sin3A and HDAC. The crystal structure of C2H2-type zinc finger of DPF2presents a canonical C2H2fold, which contains a short antiparallel β-sheet, where β1(209-211) and β2(215-218) strands are connected by β-turn(C211DIC214) and a a helix(221-230). Several conserved residues, including Lys207, Lys216and Arg217constitute a positively charged surface in C2H2domain, which implicates that it has the potential to bind DNA. The side chain of Y209, C211, C214, K216, Y218, L224, H227and H232form the hydrophobic core of DPF2. The crystal structures of different epigenetic modification reading proteins indicate that the proteins usually form a hydrophobic surface to recognize the epigenetic modification, whereas the structures of the hydrophobic core are not the same in different epigenetic modifications.The C2domain of ITSN-2L and Rab3B are two important proteins in scaffolding protein family. The crystal structure of ITSN-2L C2domain exhibits a typical C2domain fold consisting of a stable β-sandwich topology with flexible loops, and a single α-helix(residues1626-1636). The sequence and structural alignment of ITSN-2L C2domain against with other members of C2domain protein family indicate its vital cellular roles in membrane trafficking, the generation of lipid-second messengers and activation of GTPases. The crystal structure of inactive form of Rab3B exhibits a typical GTPase fold consisting of seven-stranded β, comprised of six parallel strands and one antiparallel strand, surrounded by six α helixes. The multiple sequence and crystal structure alignments of different Rab3proteins show a highly conserved switch region with the subtle distinctions in switch I region, while N-and C-terminals of the proteins are hypervariable in length and sequence. The crystal structure alignments of active and inactive form of Rab3proteins present that the significant differences are also observed switch Ⅰ and switch Ⅱ regions. These results provide a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The crystal structures of different scaffolding proteins indicate that the proteins form a specific charge distribution surface or a hydrophobic core to recognize downstream substrate in different cellular processes. Looking for exact structural mechanisms of scaffolding proteins requires further biological functional studies.Research of this paper offered some theorecical basis and thoughts for further understanding the mechanisms of the reading proteins of epigenetic modification and scaffolding proteins in membrane-associated molecular trafficking, signal transduction pathways, reading of post-translational modification and so on.