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Hands-on Course inComputational Structural

Biology and MolecularSimulation

BIOP590C/MCB590CEmad Tajkhorshid

Center for Computational Biology and BiophysicsEmail: emad@life.uiuc.edu or tajkhors@uiuc.edu

Course Details• Lectures: 1115 Siebel Center

Mon. 1/22, 1/29, 2/5, 2/12, 2/19, 2/26• Computer Labs: MCB Learning Center - 425

Natural History BuildingWed. 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%

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Course Materials

• Lectures in PDF:– www.life.uiuc.edu/emad/biop590c/

• 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 ownlaptop/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 andanalysis, Steered MD

• Day 4: Parameters and topology information

• Day 5: Simulating membrane channels andartificial model channels

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Why do we need to look atproteins in atomic detail?

How can we look at them bestand use the information?

ATP-SynthaseOne shaft, two motors

Soluble part, F1-ATPase-Synthesizes ATP when torque is appliedto it (main function of this unit)-Produces torque when it hydrolyzesATP (not main function)

Membrane-bound part,F0 Complex- Produces torque when positive protongradient across membrane(mainfunction of this unit)- Pumps protons when torque is applied(not main function)

~ 80 Å

~ 200 Å

~ 60 Å

~ 60 Å

~ 100Å

Torque is transmitted between the motors via the central stalk.

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Assembling ATP Synthase F1

• 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 + 10.5 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 F1

central stalk, γδε

applied torque

Torque is applied to the central stalk atoms at the F1-Fointerface to constrain their rotation to constant angularvelocity ω = 24 deg/ns.

0.0 to 5.0 ns (0 to 120 deg) oftorqued F1 rotation, ω = 24 deg/ns.

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Rotation Produces Synthesis-like eventsAround 3.0 – 3.5 ns (72 – 84 deg) of rotation, we observe:

• slowed torque transmission along central stalk• opening and closing motions as expected

aver

age

rota

tion

(deg

)

time (ns)stalk height

(Å)

βTP opens

βE closes

βDP does neither

At 3.5 ns (84° rotation)

Rotation Produces Synthesis-like Events

Consistent with unbinding of ATP fromthe βTP catalytic site

βTPThr163-OGto

βTPPγ

time(ns)

βTPArg189-Czto

βTPPγ

dist

ance

(Å )

3.6

4.2

4.8

5.4

6.0

0 ns: active site closed

3 ns: active site open

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reactionsite

γ

β αin situ quantum (QM/MM)

chemistry calculation

Reaction Mechanism of ATP Hydrolysis

Molecular Dynamics SimulationsProtein: ~ 15,000 atomsLipids (POPE): ~ 40,000 atomsWater: ~ 51,000 atomsTotal: ~ 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 CPUs @ NCSA

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Complete description of the conduction pathway

Selectivityfilter

Cons

triction

reg

ion

Selectivityfilter

Hydrophobicchannel

Water Permeation in Aquaporins

Download the movie from the Nobel Prize web site or from www.ks.uiuc.edu/Research/aquaporins

106,000 atoms5 ns simulation

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• Platforms:– Unix (16 builds)– Windows– MacOS X

• Display of largebiomolecules and simulationtrajectories

• Sequence browsing andstructure highlighting

• Multiple sequence - structureanalysis

• User-extensible scriptinginterfaces for analysis andcustomization

VMD - www.ks.uiuc.edu/Research/vmd

The program is used very frequently for preparation andanalysis of modeling

Focus on two proteinsUbiquitin

Bovine Pancreatic Trypsin Inhibitor (BPTI)

UbiquitinBPTI

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Ubiquitin• 76 amino acids

• highly conserved

• covalently attaches toproteins and tags themfor degradation

• other cell traficking

• Glycine at C-terminal attaches to the Lysine onthe protein by an isopeptide bond.

• it can attach to other ubiquitinmolecules and make apolyubiquitin chain.

There are 7 conserved lysine residues

in ubiquitin.

Two ubiquitins attached together through LYS 48.LYS 63 and LYS 29 are also shown there.

Lys48

Lys63

Lys29

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Mono-ubiquitylation versus multi-ubiquitylation

Marx, J., Ubiquitin lives up its name, Science 297, 1792-1794 (2002)

Protein Data Bank

Format of a PDB file

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Inspect ubiquitin with VMD

Basics of VMDLoading a Molecule

New Molecule

Browse

Load

Molecule file browser

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Basics of VMD

Rendering aMolecule

Draw styleSelected Atoms

Current graphical representation

Coloring

Drawing method

Resolution, Thickness

Basics of VMDChange rendering style

CPK tube cartoon

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Basics of VMD

Multiplerepresentations

Create Representation Delete Representation

Current Representation

Material

Left: Initial and final states ofubiquitin after spatial alignmentRight (top): Color coding ofdeviation between initial and final

VMD Scripting

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Beta Value

Structure

T: Turn E: Extended conformation H: Helix B: Isolated Bridge G: 3-10 helix I: Phi helix

List of the residues

Zoom

VMD Sequence Window

List of VMD FeaturesTcl scripts - example

Atomselect command

Structure of a PDB File

PDB

Making movies

Making paper quality figures