Biomacromolecular speleology
Most substrate-enzyme and ligand-receptor interactions in proteins take place inside clefts or cavities. Studying cavities ("biomacromolecular speleology", for short) may give insight into the mechanism of such interactions and might thereby help in the design of new ligands, substrates or inhibitors.
Many programs exist with which one may detect and/or delineate and/or measure and/or display cavities (see ref. 1 and papers cited therein). However, since we needed a program which does all of this, does it quickly and interfaces to O (2), we were forced to write our own: VOIDOO (1). Since its conception, about a year ago, VOIDOO has evolved into a multi-functional tool which is in use on a routine basis in our lab and elsewhere.
DESCRIPTION
In brief, VOIDOO has the following capabilities:
* detection of a specific void or all voids inside a
biomacromolecular complex
* detection of certain cavities which are connected
to the "outside world"
* delineation of cavities (i.e., finding their extent
in space)
* measurement of cavity volumes
* generation of plot files for O which enable visualisation
of cavities
* generation of molecular surface plot files for O
* measurement of molecular volumes
Detecting cavities which are connected to the "outside world" is non-trivial. We have implemented a method (1) which we call atomic fattening: if a certain cavity is "open" while the atoms have their normal Vanderwaals radii, we gradually increase all radii, until the cavity either vanishes or becomes a real void. In order to discern these different types of cavity, we use the following operational definitions:
* a void is a cavity which is completely surrounded
by the protein and which is
therefore closed off from the outside world;
* an invagination is a cavity which is connected to
the outside world, but
which would be closed off if the atomic radii were increased;
* a pocket is a cavity which is connected to the outside
and which cannot be
closed off by increasing the atomic radii.
VOIDOO will detect voids and invaginations, but it cannot
pick pockets. Note
that the definition of the extent of an invagination
is subjective and therefore
more or less arbitrary (where does the cavity end and
the outside world
begin?).
VOIDOO can be set to measure and display cavities in three different modes:
(1) Vanderwaals cavity: the cavity comprises the complement
of the
Vanderwaals surface of the surrounding atoms;
(2) Probe-accessible cavity: the cavity comprises all
of space that can be
accessed by the centre of a probe sphere (default);
(3) Probe-occupied cavity: the cavity comprises all
of space that can be
occupied by a probe sphere (slow).
The input to VOIDOO consists of three parts:
(1) a library which defines which residue types are
considered to be part of
the protein (or other molecule) as well the Vanderwaals
radii of various atom
types;
(2) an ordinary PDB file;
(3) parameters which determine what the program should
do and how.
An example of part of a library file is given below:
REMA *** AMBER van der Waals radii *** ELEM ' N' 1.75 ELEM ' C' 1.85 ... REMA CH2 = 1.925 SPAT 'SER* CB ' 1.925 ... REMA *** allowed residue types *** RESI 'ALA' ... RESI 'VAL' RESI 'CPR' ENDWe distribute two protein-oriented libraries, one containing Vanderwaals radii taken from the Amber force-field and one containing MS-like radii. Libraries for other types of molecules (DNA, oligosaccharides etc.) are easy to make.
The output of VOIDOO, in a cavity-detection run, also consists of three parts:
(1) normal screen output regarding the program's operation;
(2) a log file containing a summary of the results (extent
of each cavity, its
volume, its centre of gravity and a list of non-protein
atoms that lie inside it as
well as protein atoms that border on it);
(3) files for use with O, namely for each cavity: a
map file which can be
displayed and a macro which draws all residues inside
the cavity as well as
those that line the surface of the cavity. The map
files are written in EZD-format (EZD ~ "easy density";
this is a formatted
ASCII file which can be
converted into DSN6-format or read into O directly).
Figure 1 is an example of an O display, showing the cavity as a chicken-wire contour (on SGI workstations, cavities may also be rendered as semi-transparent surfaces), the ligand inside the cavity (fat lines) and the residues that surround it. This example pertains to cellular retinol-binding protein, whose structure was recently solved in our lab (3).
AVAILABILITY
VOIDOO is one in a series of "O-dalisques",
i.e. programs that work in
conjunction with O. VOIDOO runs on SGI, ESV and DEC
ALPHA/OSF1
workstations. For more information, contact TAJ (preferably
via E-mail:
"alwyn@xray.bmc.uu.se").
REFERENCES
(1) G.J. Kleywegt & T.A. Jones, "Detection,
delineation, measurement and display of cavities
in macromolecular structures", submitted for publication.
(2) T.A. Jones, J.Y. Zou, S.W. Cowan & M. Kjeldgaard,
"Improved methods for building
protein models in electron density maps and the location
of errors in these models", Acta
Cryst. A47 (1991), 110-119.
(3) S.W. Cowan, M.E. Newcomer & T.A. Jones, "Crystallographic
studies on a family of
cellular lipophilic transport proteins. Refinement
of P2 myelin protein and the structure
determination and refinement of cellular retinol-binding
protein in complex with all-trans-
retinol", J. Mol. Biol. 230 (1993), 1225-1246.
Latest update at 12 February, 1998.