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Assignment for Molecular Modeling Practical

This tutorial provides a short introduction to the set-up and running of Molecular Dynamics (MD) simulations of small peptides. The protocol used is a suitable starting point for investigation of peptides, provided that the system does not contain non-standard groups. At the end of the tutorial, the student should know the steps involved in setting up and running a simulation, including some reflection on the choices made at different stages. Besides, the student should know how to perform quality assurance checks on the simulation results and have a feel for methods of analysis to retrieve information. Finally, the student should be able to define and apply distance restraints for MD simulations based on data deposited in the Protein Data Bank.

Specification of NMR Restraints as deposited in the Protein Data Bank

The Protein Data Bank is a repository for structures obtained by X-ray and NMR spectroscopy. Apart from final coordinates, other data may also be deposited, such as distance restraints. The deposited data adhere to standards that are often used in different softwares for data analysis and/or modeling and calculations using the deposited data.

One of the formats used for NMR distance restraints, and the format most easily converted to distance restraints in the GROMACS molecular dynamics simulation package is the .mr format. This format for describing NOE distance restraints is described at the website of the CNS suite of programs. CNS stands for Crystallography and NMR System. An example that uses distance restraints is given in this section of the tutorial.

It is wise to run this simulation in a separate directory. Copy the files you need to that directory and proceed... Also NOTE that the protein may be solvated differently in the unfolded state than in the unfolded state. If all is well, all you may need to change in the file protein.top is to change the number of water molecules. It should be 1775.

Homework assignment for the Structural Biology Course

1. Based on the file 1l2y.mr that was deposited to the PDB by Neidigh et al., prepare a file with distance restraints for use in GROMACS with the AMBER force field between atoms of the Trp side chain (starting from C-beta) with any atom belonging to a residue that is five or more residues removed from Trp in the primary structure.
Apply a force constant of 1000 kJ/(mol nm2) for unique H-H pairs, i.e. pairs of H-atoms that are each involved in only one NOE. If a H-atom is involved in multiple NOEs, apply a force constant of 100 kJ/(mol/nm2) to each pair this H-atom is involved in.
Give the file that lists the restraints in GROMACS format, the name TrpDisRe-sXXXXXXX.itp, where XXXXXXX are the digits of your student number.

2. Use the file with the distance restraints you defined in a simulation of the Trp cage, starting from the unfolded conformation given in the coordinate file trp-unfolded.gro, to run an MD simulation including those distance restraints (and no others!) for 200 ps under the same conditions (temperature, pressure, strength of restraints) as the simulation with all distance restraints. Prepare a .pdb file that contains ONLY the protein coordinates of the FINAL structure of the simulation, and give it the name TrpCage-sXXXXXXX.pdb. where XXXXXXX are the digits of your student number.

3. Prepare eps images of the r-6 weighted distance analysis for the first 50 ps and for the final 50 ps (i.e. TWO images) of the simulation with the selected distance restraints and name them Idist-sXXXXXXX.eps and Fdist-sXXXXXXX.eps (I for initial, F for final), again with XXXXXXX the digits of your student number.

4. Send an email to A.H.de.Vries@rug.nl with the four files you prepared as attachments.