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COILED COIL PROTOCOLS

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|--Generating Sequence Files

|--Building Coiled Coil Models

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Generating Sequence Files

The process of coiled coil building and free energy computation has been made easier by including certain Sequence Files. These are the coiled coil sequence of your model in three different formats.

The *.seq_file tree-letter Format: list the sequence with a constant number of characters. This is good for displaying tables that are more easily readable.

 For example:
 GLY  9
 MET 10
 .
 .
 LEU100

The *.seq tree-letter Format: list the sequence with a variable number of characters depending on how large the number is. This is used for naming the torsional angles of each residue.

 For example:
 GLY9
 MET10
 .
 .
 LEU100

The *.SEQ one-letter Format: list the sequence with one-letter code. This is best read by computer programs. SCWRL3.0 uses such an input (Canutescu, A. A.; Shelenkov, A. A.; Dunbrack, R. L., Jr. “A graph-theory algorithm for rapid protein side-chain prediction“ Protein Sci. 2003, 12, 2001−2014).

The sequences are generated by either the seq_read.f or the heptad.f program in the seq_read directory.

For the seq_read.f it is assumed you know the heptad assignment of the coiled coil sequence. You will be asked to give a heptad "abcdefg" assignment to the first residue in the sequence.

The program will read tree-letter or one letter code format. Research papers will usually display one-letter code for amino acid sequences and several online programs give such output. The three-letter code can be copied from the SEQRES lines on PDB files.

For the heptad.f you may or may not know the heptad assignment of the coiled coil sequence. The program will give you the option of letting it give heptad assignments to the amino acids using Lupas' scoring matrix (Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting Coled Coils from Protein Sequences, Science 252:1162-1164).

It is a good practice to add ACE and CBX capping groups. Since SCWRL3.0 does not recognize ACE and CBX, these residues should be treated as GLYCINE in the *.SEQ file.

Building Coiled Coil Models

The coiled coil structures are generated by the coil_builder.f (parallel) or the anti_coil.f(antiparallel) program in the coil_builder directory. This programs don't require any input files because all parameters are hard coded into them.

Monomer: Single helix with 3.5 residues per turn.

Dimer: from 2ZTA

Trimer: from 1CE0

Tetramer:

Pentamer:

The coil_builder.f you will be asked to give the number of residues oligomeric state, and heptad "abcdefg" assignment of the first residue in the sequence. The ACE and CBX capping groups are added to the sequence and don't have to be included in the number of residues given by the user. Thus the three residue sequence GLY LEU GLY would be:

 ACE  1
 GLY  2
 LEU  3
 GLY  4
 CBX  5

The program