Supporting Information for. Models for the Metal Transfer Complex of the N-terminal Region of CusB and. CusF
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1 Supporting Information for Models for the Metal Transfer Complex of the N-terminal Region of CusB and CusF Melek N. Ucisik, Dhruva K. Chakravorty, and Kenneth M. Merz Jr. * Department of Chemistry and Quantum Theory Project, University of Florida, 2328 New Physics Building, P.O. Box , Gainesville, Florida , United States Department of Chemistry, University of Illinois at Urbana-Champaign, 6 South Mathews Avenue, Urbana, IL Department of Chemistry, University of New Orleans, 2 Lake Shore Drive, New Orleans, LA 7148, United States Institute for Cyber Enabled Research, Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 South Shaw Lane, East Lansing, Michigan , United States
2 15 RMSD (Å) 1 5 MMM: 6 µs MMH: 4 µs Time (ns) Figure SI1. RMSD profiles of the MMM model over the simulation time of 6µs and the MMH model over 4 µs. The MD simulation of the MMM model was run on upon observing that CusB-NT and CusF were in a closer interaction in the MMM model rather than in the MMH model MMH: 4 µs MMM: 4 µs MMM: 6 µs RMSF (Å) Residue Number Figure SI2. RMSF profiles of the MMM model over both 4 µs (black) and 6 µs (orange), and the MMH model over 4 µs (red).
3 3 25 K32CA-P84CA distance/ MMM (6 µs) Distance between the COM s of the residues and 75-87/ MMM (6 µs)) K32CA-P84CA distance/ MMH Distance between the COM s of the residues and 75-87/ MMH Time (ns) Figure SI3. Distances of the M21-M36 loop of CusB-NT and the open flap of CusF expressed in terms of the separation between their centers of mass (red) and the separation between the CusB-NT residue K32 and the CusF residue P45 (black). Solid lines stand for the results from the MMM model and the dashed lines represent those from the MMH model. The separation expressed by both of these properties is smaller in the MMM model compared to the MMH model K32CA-P84CA distance/ MMM Distance between the COM S of the residues and 75-87/MMM K32CA-P84CA distance/ MMH Distance between the COM s of the residues and 75-87/ MMH K32CA-P84 CA distance/ MMM (6 µs) Distance between the COM s of the residues and 75-87/ MMM (6 µs)) Figure SI4. Histograms for the distances of the M21-M36 loop of CusB-NT and the open flap of CusF expressed in terms of the separation between their centers of mass (red and yellow-dashed) and the separation between the CusB-NT residue K32 and the CusF residue P45 (black and yellow-solid).
4 15 12 MMM (6 µs) MMH (4 µs) Angle Time (ns) Figure SI5. The angle involving the center of mass of CusB-NT s M21-M36 loop, Cu(I), and the center of mass of CusF s open flap over the entire production run. Black represents the values from the MMM model and red from the MMH model Angle MMM (4 µs) MMH (4 µs) MMM (6 µs) Figure SI6. The histograms for the angle involving the center of mass of CusB-NT s M21-M36 loop, cu(i), and the center of mass of CusF s open flap over the entire production run of 4 µs. Black represents the values from the MMM model and red from the MMH model.
5 NZ-85OE1 32NZ-85OE2 32NZ-82O 26NH1-85OE1 26NH1-85OE2 33N-82O 33OG-83NE1 26NH2-85OE1 26NH2-85OE2 22OH-87N 22OH-87OG1 Figure SI7. Distances of possible hydrogen bonding partners on the CusB-NT M21-M36 loop and the CusF open flap. Solid lines express the probed distances in the MMM model over 4µs and the dashed lines stand for the distances obtained from the same model over 6 µs. Involved residues are the following: K32 of CusB-NT ( 32 ), D46 of CusF ( 85 ), N43 of CusF ( 82 ), R26 of CusB-NT ( 26 ), S33 of CusB-NT ( 33 ), W44 of CusF ( 83 ), Y22 of CusB- NT ( 22 ), and T48 of CusF ( 87 ). NZ, NH1, NH2, and NE1 represent side chain nitrogens while OE1, OE2, OG, and OH stand for side chain oxygens. N is a backbone nitrogen and O is a backbone oxygen.
6 MMM (4 µs) MMH MMM (6 µs) Figure SI8. Histograms for the distance between the centroids of the phenyl ring of CusB- NT s F35 and of the phenyl part of the indole ring of CusF s W44. Results for the MMM model are shown in black/yellow and for the MMH in red.
7 Table S1. Amino acid numbering for the CusB and CusF parts of the system. System Separate Cumulative CusB-NT 1:51 1:51 CusF 13:88 52:127
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