Practical GK-10

Structural alignment

Aims

• To reinforce the concepts of three-dimensional transformations in the context of structure alignment.
• To revise some of the concepts in protein structure alignment.

Objectives

After this practical you will:

• be aware of how the transformation and fitting code seen in earlier lectures and practicals can be used in structure alignment.

Exercises

1. File /chalmers/users/kemp/TDA506/practical10/two_h2_loops.pdb contains two protein fragments which have been superposed. Model 1 has ten residues and model 2 has nine residues. View these fragments in a molecular graphics program. Write down the sequences of the two models, and identify which residues in model 1 correspond with which residues in model 2.

2. In DALI:

   "An internal coordinate frame is defined by an ordered pair of SSEs (centering one SSE at the origin, aligning it with the y axis, and rotating the molecule around this axis so that the center of a second SSE is in the positive x-y plane)."
   From "Mapping the Protein Universe" by Liisa Holm and Chris Sander (Science, vol. 273, 595-602, 1996)

   Suppose that points P1n and P1c are, respectively, points at the N and C ends of a line segment representing secondary structure element S1, and that points P2n and P2c are, respectively, points at the N and C ends of a line segment representing secondary structure element S2. Describe the steps needed to transform this pair of SSEs to the internal coordinate frame.

3. A method for bringing two residues into the same frame of reference is described in the first paragraph of section 2(e) of: Taylor W.R. and Orengo C.A. (1989) "Protein structure alignment", J. Mol. Biol., 208, 1-22 (PubMed).

   1. Describe how this can be achieved using the functions in the transformation and geometry libraries.

   2. Suggest an alternative way to bring two residues into the same frame of reference.