[Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix)

Anshul Bhardwaj Anshul.Bhardwaj at jefferson.edu
Sun Apr 20 20:43:23 PDT 2014


Hi Ashok,

Chimera experts may be able to explain you how to calculate coiled-coil radius in the Chimera, nonetheless, for our purposes we have recently used the program TWISTER (Strelkov, S. V. & Burkhard, P. (2002). J. Struct. Biol. 137, 54–64.) that analyzes various coiled-coil parameters including coiled-coil radius from the pdb coordinate file. You may want to give it a try, it is very easy to use. We summarized our results in the form of table that you can find in the published article Bhardwaj, A., Casjens, SR., Cingolani, G. Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography (2014) Acta Crystallogr D Biol Crystallogr.<http://www.ncbi.nlm.nih.gov/pubmed/24531468#> 2014 Feb;70(Pt 2):342-53.

You can request the program TWISTER from Sergei V. Strelkov, sergei.strelkov at pharm.kuleuven.be


From TWISTER documentation;


Program TWISTER (2006 version)

AUTHOR
Sergei V. Strelkov
e-mail: sergei.strelkov at pharm.kuleuven.be

PURPOSE
The program TWISTER is designed to analyse the local geometry of coiled-coil (cc) structures. With the three-dimensional coordinates on input, TWISTER first traces the alpha-helical axes and then the cc axis. Thereafter the local cc parameters are determined as a function of residue number. In addition, heptad positions are assigned based on structural criteria. The current version of the program is designed to analyse
parallel coiled coils with residue numbering in different chains being in register; however, see a note on antiparallel / out-of-register coiled coils below.

REFERENCE
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.

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

SUPPORTED PLATFORMS
1. Linux: Use the executable tw2006_linux_exe.
2. Windows: You must install the free unix emulator cygwin
(www.cygwin.com) first. Make sure that you have installed
the tcsh shell (available in cygwin but not installed by default).
Then use the tw2006_cygwin_exe.
3. OSX: The current executable tw2006_osx_exe is outdated and
will only run under older versions of OSX.
4. SGI IRIX: Use tw2006_sgi_exe.

USAGE
Please use a short shell script (see twister_example.sh) to run the program, as running the program directly from command line may not work on all platforms. A sample output from this script with the GCN4 zipper trimer is provided in subdirectory /example. Please edit this example script according to your needs.

Input is a standard PDB format coordinate file. It is sufficient to input the C-alpha coordinates only. Within the shell script, the user has to specify which part of the structure to analyse (e.g. residues 101 to 151 of chains A, B and C if these form a triple-stranded coiled coil). There are two output files.  The first one is a log file that contains a table of geometrical parameters versus residue number. In addition, average values of each parameter over all residues and their standard deviations are output. The log file can be piped into the program XLOGGRAPH which is part of the CCP4 package to produce plots from the tables. Alternatively, any other graphing software can be used. The second output file includes the coordinates of all alpha-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.

DESCRIPTION OF THE LOG FILE
1. Sequence and heptad assignment
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 COILS
The 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 that
to 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:

~/myprogs/twister/twister << eof > $log
$title $infile $outfile 1 20 A B
eof

The sequence will be read from the first chain listed, in
this case chain A.

BUGS AND FURTHER DEVELOPMENT
Please report bugs and send your comments and suggestions
to sergei.strelkov at pharm.kuleuven.be


Hope this helps!

Best,

Anshul Bhardwaj



Anshul Bhardwaj, Ph.D.
Faculty, Department of Biochemistry and Molecular Biology
Manager, Kimmel Cancer Center X-ray Crystallography and Molecular Interactions
Thomas Jefferson University
233 South 10th Street, BLSB suite 822
Philadelphia, PA 19107
Tel: (215) 503-4587
Anshul.Bhardwaj at Jefferson.edu
http://www.jefferson.edu/jmc/departments/biochemistry/faculty-staff/faculty/bhardwaj.html
http://www.kimmelcancercenter.org/kcc/kccnew/research/resources/xray/index.htm
________________________________
From: chimera-users-bounces at cgl.ucsf.edu <chimera-users-bounces at cgl.ucsf.edu> on behalf of ashok rout <ashok9869 at gmail.com>
Sent: Sunday, April 20, 2014 3:10 PM
To: chimera-users at cgl.ucsf.edu Mailing List
Subject: [Chimera-users] how to calculate the core diameter of a trimer (the individual subunits of this trimer is a helix)

Hi,
 I have a transmembrane domain of a protein (20 amino acid long, single helix). The NMR derived structure comes out as a coiled-coil trimer. So can you please assists me how to calculate the core diameter of this trimer.
Regards,
Ashok

--
thanks & regards,
Ashok

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