Hands-on Course in Computational Structural Biology and Molecular Simulation BIOP590C/MCB590C. Course Details
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1 Hands-on Course in Computational Structural Biology and Molecular Simulation BIOP590C/MCB590C Emad Tajkhorshid Center for Computational Biology and Biophysics or Course Details Lectures: 1115 Siebel Center Mon. 1/22, 1/29, 2/5, 2/12, 2/19, 2/26 Computer Labs: MCB Learning Center Natural History Building Wed. 1/24, 1/31, 2/7, 2/14, 2/21, 2/28 Office hours: Fri 2-4 pm, Beckman 3009 and 3013 TA: Eric Lee (Beckman 3013) Grading Attendance 50% Homework/assignments 25% Term Project 25% 1
2 Course Materials Lectures in PDF: Tutorials and files needed: Will be installed on the LC machines can also be downloaded from the above link, Install your own VMD/NAMD on your own laptop/desktop for your term projects: MAC, PC, Linux. Course Syllabus Day 1: Visualization and basic structural analysis of biomolecules Day 2: Setting up and analyzing Molecular Dynamics Simulations Day 3: Advanced MD simulations and analysis, Steered MD Day 4: Parameters and topology information Day 5: Simulating membrane channels and artificial model channels 2
3 Why do we need to look at proteins in atomic detail? How can we look at them best and use the information? ATP-Synthase One shaft, two motors ~ 100Å ~ 200 Å ~ 80 Å Soluble part, F 1 -ATPase -Synthesizes ATP when torque is applied to it (main function of this unit) -Produces torque when it hydrolyzes ATP (not main function) ~ 60 Å ~ 60 Å Membrane-bound part, F 0 Complex - Produces torque when positive proton gradient across membrane(main function of this unit) - Pumps protons when torque is applied (not main function) Torque is transmitted between the motors via the central stalk. 3
4 Assembling ATP Synthase F 1 Start with DCCD-inhibited structure (Gibbons 2000, PDB code 1E79) Total 327,000 atoms (3325 residues, 92,000 water molecules, nucleotides, and ions). The 1.2 ns equilibration ns torque application were performed on NCSA Platinum and PSC Lemieux using up to 512 processors. Combined w/ post-equlibrations, total 18 ns, 652,000 CPU hours Torque application to F 1 Torque is applied to the central stalk atoms at the F 1 -F o interface to constrain their rotation to constant angular velocity ω = 24 deg/ns. applied torque central stalk, γδε 0.0 to 5.0 ns (0 to 120 deg) of torqued F 1 rotation, ω = 24 deg/ns. 4
5 Rotation Produces Synthesis-like events Around ns (72 84 deg) of rotation, we observe: slowed torque transmission along central stalk opening and closing motions as expected At 3.5 ns (84 rotation) average rotation (deg) time (ns) stalk height (Å) β E closes β TP opens β DP does neither Rotation Produces Synthesis-like Events Consistent with unbinding of ATP from the β TP catalytic site β TP Thr163-OG to β TP P γ 4.8 distance(å ) β TP Arg189-C z to β TP P γ 0 ns: active site closed 3 ns: active site open time(ns) 5
6 Reaction Mechanism of ATP Hydrolysis β α in situ quantum (QM/MM) chemistry calculation reaction site γ Molecular Dynamics Simulations Protein: ~ 15,000 atoms Lipids (POPE): ~ 40,000 atoms Water: ~ 51,000 atoms Total: ~ 106,000 atoms NAMD, CHARMM27, PME NpT ensemble at 310 K 5 ns run of wild-type protein 2 days /ns 48-proc Linux cluster 0.35 days /ns 64 NCSA 6
7 Complete description of the conduction pathway Constriction region Selectivity filter Water Permeation in Aquaporins Hydrophobic channel Selectivity filter 106,000 atoms 5 ns simulation Download the movie from the Nobel Prize web site or from 7
8 VMD - Platforms: Unix (16 builds) Windows MacOS X Display of large biomolecules and simulation trajectories Sequence browsing and structure highlighting Multiple sequence - structure analysis User-extensible scripting interfaces for analysis and customization The program is used very frequently for preparation and analysis of modeling Focus on two proteins Ubiquitin Bovine Pancreatic Trypsin Inhibitor (BPTI) Ubiquitin BPTI 8
9 76 amino acids highly conserved Ubiquitin covalently attaches to proteins and tags them for degradation other cell traficking Glycine at C-terminal attaches to the Lysine on the protein by an isopeptide bond. it can attach to other ubiquitin molecules and make a polyubiquitin chain. There are 7 conserved lysine residues in ubiquitin. Lys48 Lys29 Lys63 Two ubiquitins attached together through LYS 48. LYS 63 and LYS 29 are also shown there. 9
10 Mono-ubiquitylation versus multi-ubiquitylation Marx, J., Ubiquitin lives up its name, Science 297, (2002) Protein Data Bank Format of a PDB file 10
11 Inspect ubiquitin with VMD Basics of VMD Loading a Molecule New Molecule Molecule file browser Browse Load 11
12 Basics of VMD Current graphical representation Rendering a Molecule Draw style Coloring Drawing method Selected Atoms Resolution, Thickness Basics of VMD Change rendering style CPK tube cartoon 12
13 Basics of VMD Create Representation Delete Representation Current Representation Multiple representations Material VMD Scripting Left: Initial and final states of ubiquitin after spatial alignment Right (top): Color coding of deviation between initial and final 13
14 VMD Sequence Window Beta Value List of the residues Structure Zoom T: Turn E: Extended conformation H: Helix B: Isolated Bridge G: 3-10 helix I: Phi helix List of VMD Features Tcl scripts - example Atomselect command Structure of a PDB File PDB Making movies Making paper quality figures 14
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