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Program TWISTER (2006 version)
Sergei V. Strelkov
e-mail: sergei.strelkov@pharm.kuleuven.be

local cc parameters are det the cc axis. Thereafter the he structural criteria. heptad positions are assigned based on antiparallel / out-of-register coiled coils below.fferent

Strelkov, S.V., and Burkhard, P. (2002) Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J. Struct. Biol. 137, 54-64. Please consult this publication for full description of program function and definitions.

The program executables can be obtained from the author on request. The program is written in standard C programming language.

1. Linux: Use the executable tw2006_linux_exe.

in subdirectory /examplhe GCN4 zipper trimer is providedput . Please edit this example script according to your needs.

residues 101 to 151 of chains A, B and C if these for (e.g.
their standard deviath parameter over all residues and on,
file includes the coordinates of all alp The second output
a-helix axes and
of the cc axis. The axes appear as polypeptide chains
containing C-alpha atoms only and can be visualised with
any biomolecular graphics software such as RASMOL or PyMol.

TWISTER assigns the heptad positions on the basis of the structure. First the a and d positions are assigned based on their proximity to the cc axis. The residues for which the heptad position could not be assigned are labelled 'z'.
2. Coiled-coil parameters
These are tabulated for every residue with the exception of the N- and C-terminal residues.
CC_PHASE: cc phase in degrees relative to zero phase at the first residue.
CC_RAD: local cc radius in A.
CC_RISE: cc rise per residue (measured along the cc axis).
CC_PIT: local cc pitch calculated as 2Pi*CC_RIS/CC_DANG. If the local cc geometry is right-handed, the pitch value is followed by a letter 'R'.
CC_DANG: increment of the cc phase per residue. This is negative for a left-handed geometry and positive for a right-handed one.
POS: heptad position.
CR_ANG: the angle (first introduced by F. Crick) which defines the phase of the Calpha atom relative to the cc axis.
A_RAD: alpha-helical radius.
A_RIS: alpha-helical rise.
RES/TUR: number of residues per one alpha-helical turn.
A_DANG: increment of the alpha-helical phase per residue.
AXIS_CUR: curvature of the alpha-helical axis in 1/A.
3. Crick angles for residues in a and d positions.
4. A table for XLOGGRAPH.
A NOTE ON ANTIPARALLEL AND OUT-OF-REGISTER COILED COILSThe current version of the program is designed to work on parallel coiled coils with residue numbering in all chains being in register. However, both these limitations can be overcome by renumbering the side chains manually so thatto bring them into register. In an antiparallel structure, this would require inverting some chain(s).Here is an example. Suppose you want to analyse a two-stranded antiparallel coiled coil consisting of residues A1 to A20 (downward chain) and B51 to B70(upward chain), with residues A1 and B70 being in register. Then you have to renumber chain B so that residue B70 becomes B1, B69 becomes B2 etc. (renumbering Calphas suffices). Thereafter run TWISTER as follows:

/public/apps/twister/twister << eof > $log
$title $infile $outfile 1 20 A B
The sequence will be read from the first chain listed, in this case chain A.

Please report bugs and send your comments and suggestions to sergei.strelkov@pharm.kuleuven.be

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