Pipeline publication

[…] b'Kir2.1 channel gating unfolds in a step-by-step process as follows. First, with the upward motion of the CTD, the C-linker forms a new helix and the Kir2.1 channel achieves an \xe2\x80\x9cactivated\xe2\x80\x9d state but the pore remains in the closed state. Second, the kink of the C-linker triggers the rotation of the CTD which pulls the pore open. Moreover, we identified a series of interaction networks that controls the PIP2-induced conformational changes during Kir channel gating. Based on the data, a brand new gating model is proposed which will shed light on understanding the molecular mechanism of PIP2 gating of Kir channels., Homology models of the full-length mouse Kir2.1 channel were performed using the SWISS-MODEL server. The target sequences were taken from Genbank (http://www.ncbi.nlm.nih.gov/Genbank/). The template structures were the chicken Kir2.2 (PDB code: 3JYC and 3SPI), and the mouse Kir3.2 (PDB code: 3SYQ). These homology models were based on chain A of the template structures, in which the two missing loops, one that connects the N-terminal beta-strand and the slide helix, and one that connects the two transmembrane alpha-helices, were completed. All the models were evaluated with QMEAN (The QMEAN4 score is a composite score consisting of a linear combination of 4 statistical potential terms (estimated model reliability between 0\xe2\x80\x931). The pseudo-energies of the contributing terms are given their Z-scores with respect to scores obtained for high-resolution experimental structures of similar size solved by X-ray crystallography. The members of the inwardly rectifying K+ channel family exhibit high degree of sequence similarity. Due to high sequence homology (about 78%, 77% and 53% sequence identity to chicken Kir2.2 and mouse Kir3.2 respectively), the QMEAN4 score was 0.79, 0.566 and 0.545 respectively and QMEAN Z-score was \xe2\x88\x924.54, \xe2\x88\x923.36 and \xe2\x88\x923.66 respectively. Each model was compared to its template to verify that the modeling step had not significantly altered backbone and side chain conformation., For the full-length Kir2.1 channels simulation, the channels were immersed in an explicit palmitoyloleoyl-phosphatidylcholine (POPC) bilayer generated by the VMD membrane package. The whole system was then solvated, and K+ and Cl\xe2\x88\x92 of ~150\xe2\x80\x89mM were positioned randomly among the solvent to neutralize the system. We built three systems (Closed, Activated, and Open states). Each system involved ~140,000 atoms in the MD simulation. Full three-dimensional periodic boundary conditions were used. Each system was in a rectangular box with the size of 101\xe2\x80\x89\xc3\x97\xe2\x80\x8998\xe2\x80\x89\xc3\x97\xe2\x80\x89156\xe2\x80\x89\xc3\x853 (Closed state), 101\xe2\x80\x89\xc3\x97\xe2\x80\x8999\xe2\x80\x89\xc3\x97\xe2\x80\x89156\xe2\x80\x89\xc3\x853 (Activated state), and 104\xe2\x80\x89\xc3\x97\xe2\x80\x89105\xe2\x80\x89\xc3\x97\xe2\x80\x89153\xe2\x80\x89\xc3\x853 (Open state), respectively. The solvated systems then underwent four equilibration steps: (i) 4\xe2\x80\x89ns of equilibration with melting of lipid tails, (ii) the entire protein was fixed for 5\xe2\x80\x89ns, enabling reorganization of t' […]

Pipeline specifications

Software tools SWISS-MODEL, QMEAN, VMD
Diseases Hamartoma Syndrome, Multiple, Neoplastic Syndromes, Hereditary