caa a22 4500 605513376 CHVBK 20210128100700.0 cr unu---uuuuu 210128e20150501xx s 000 0 eng 10.1007/s00894-015-2664-7 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2664-7 Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation [Elektronische Daten] [Qianjun Liu, Guodong Hu, Zanxia Cao, Jihua Wang, Haifeng Chen] DSS1 is a small acidic intrinsically disordered protein (IDP) that can fold upon binding with PCID2 TREX-2. The resulting complex plays a key role in mRNA export. However, the binding mechanism between DSS1 and PCID2 is unsolved. Here, three independent 500-ns molecular dynamics (MD) simulations were performed to study the DSS1-PCID2 binding mechanism by comparing apo-PCID2 and bound PCID2. The results show that the conformational variation of bound PCID2 is smaller than that of apo-PCID2, especially in the binding domain of two helices (helix IV and VIII). The probability of coil formation between helix III and helix IV of bound PCID2 increases, and a short anti-parallel β-sheet forms upon DSS1 binding. The decomposition of binding free energy into protein and residue pairs suggests that electrostatic and hydrophobic interactions play key roles in the recognition between DSS1 and PCID2. There is a hydrophobic core of seven residues in DSS1 favorable to the binding of PCID2. These analytical methods can be used to reveal the recognition mechanisms of other IDPs and their partners. Figure Differences of second structure of PCID2 in bound and unbound states. The interaction surface between the helix VIII of PCID2 and helix of DSS1 Springer-Verlag Berlin Heidelberg, 2015 PCID2 protein nationallicence Molecular dynamics simulation nationallicence Conformational changes nationallicence Binding free energy nationallicence Liu Qianjun Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut Hu Guodong Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut Cao Zanxia Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut Wang Jihua Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut Chen Haifeng State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 200240, Shanghai, China aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/5(2015-05-01), 1-9 1610-2940 21:5<1 2015 21 894 https://doi.org/10.1007/s00894-015-2664-7 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2664-7 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Liu Qianjun Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut NATIONALLICENCE 700 1- Hu Guodong Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut NATIONALLICENCE 700 1- Cao Zanxia Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut NATIONALLICENCE 700 1- Wang Jihua Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, College of Physics and Electronic Information, Dezhou University, 253023, Dezhou, China aut NATIONALLICENCE 700 1- Chen Haifeng State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 200240, Shanghai, China aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/5(2015-05-01), 1-9 1610-2940 21:5<1 2015 21 894