Conformational And Dynamical Characteristics Of Intrinsically Disordered Protein DSS1Which Plays A Multifunctional Role

DSS1, an intrinsically disordered protein, is closely related with cancer in mammals thatregulates the functional integrity of multiple protein complexes as a “molecular glue”. Thecomplex of DSS1and PCID2as a component of TREX-2complex plays an important role inmRNA export. The DSS1-BRCA2interaction plays a significant role in the recombinationalrepair pathway. DSS1shows different conformations in combination with two differentproteins, and the experimental information indicated that the function of DSS1protein is tostabilize the structure of PCID2and BRCA2. But up to now, the full details and mechanismsof the DSS1-PCID2interaction and the DSS1-BRCA2interaction have been known little. It isa better method to understand the interaction of intrinsically disordered proteins at atomiclevel by molecular dynamics simulation. Molecular dynamics simulation can not onlycompare the conformational changes of DSS1with different proteins, but also providesignificant insight into understanding how to exercise the functions of DSS1.Molecular dynamics simulations can be used to study biological macromolecules, andhas an important practical significance in the study of intrinsic disorder protein. We utilizedmolecular dynamics simulations to analyze the coupling between binding and conformationalchange in PCID2-DSS1complex and BRCA2-DSS1complex. The conformational changeswere assessed by the root mean square deviations (RMSD) of Cα atoms, the root mean squarefluctuation (RMSF) of the Cα atoms, principal components analysis (PCA) and tertiarycontact. The mechanism of conformational change was analyzed with the probability of helixformation and the decomposition of binding free energy.1. The disordered protein DSS1as a component of TREX-2complex affects the stabilityof PCID2. The results show that conformational variation of bound PCID2is smaller than thatof apo-PCID2, especially in the binding domain of two helices (helices Ⅳ and Ⅷ). Thehelix of DSS1and helix Ⅷ of bound PCID2are more stable while DSS1binding the cleftbetween helix Ⅳ and helix Ⅷ of bound PCID2, and the coil of DSS1tend to form thesecondary structure that more stable. The decomposition of binding free energy into proteinand residue pairs suggests that electrostatic and hydrophobic interactions play key roles in therecognition between DSS1and PCID2. There is a hydrophobic core formed by seven residues,which is favorable for DSS1binding to PCID2. These results are in good consistence withexperimental data. The MD simulations indicates that DSS1affect the stability of PCID2, which causes the more stability for PCID2.2. The disordered protein DSS1affects the stability of helical domain of BRCA2. Theconformational free energy of DSS1reduces when BRCA2COOH-terminal domain bound toDSS1. The disordered protein DSS1tends to form stable secondary structure. The number ofhydrogen bonds increases in the helical domain of BRCA2, helix Ⅸ and helix Ⅹ of helicaldomain of BRCA2in complex are more stable than those in unbound state. But it is notobvious for the OB1domain of BRCA2protein.3. The conformation of the disordered protein DSS1is different in combination withPCID2and BRCA2. Apo-DSS1is highly flexible, the results are in good agreement with theproperty of the intrinsically disordered protein. The helix of DSS1is more stable and thesecondary structure of coil of DSS1become more regular when DSS1COOH-terminaldomain (Residues:38-67) bound to PCID2. The probabilities of secondary structures analysisshows DSS1tends to form the β-sheet and turn when DSS1is in complex. The secondarystructures of DSS1are mainly coil and turn when COOH-terminal domain (Residues:7-25)and N-terminal domain (Residues:37-45,50-63) of DSS1bound to BRCA2. The comparisonof DSS1in PCID2-DSS1complex and in BRCA2-DSS1complex indicated that the structureof DSS1is different in two complexes and the secondary structure of DSS1are more stabilityin two complexes than in unbound states.The main content is divided into five chapters. The first chapter is introduction. It mainlyintroduces the research of DSS1with different proteins, including the relationship betweenDSS1and diseases, DSS1protein’s molecular structure and its role in the disease, thebiological effects produced by lack of DSS1. The second chapter is brief introduction ofmolecular dynamics simulation, including the basic theory of molecular dynamics simulation,the software of molecular dynamics simulation, GROMACS software, analysis methods, theapplication and development of molecular dynamics simulation. The third and fourth chapteris the results and analysis for how does the disordered protein DSS1influence the stability ofPCID2and BRCA2. The last chapter is the summary and prospect.