HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures
© Ho and Gruswitz; licensee BioMed Central Ltd. 2008
Received: 26 August 2008
Accepted: 14 November 2008
Published: 14 November 2008
An accurate rendering of interior surfaces can facilitate the analysis of mechanisms at atomic-level detail, such as the transport of substrates in the ammonia channel. In molecular viewers, one must remove the exterior surface that obscures the channel surface by clipping the viewing plane or manually selecting the channel residues in order to display a partial surface. Neither method is entirely satisfactory, as unwanted additional pieces of surfaces are always generated.
To cleanly visualize a channel surface, we present HOLLOW, a program that generates a "casting" of the interior volume of the protein as dummy atoms. We show that the molecular surface of the dummy atoms closely approximates the channel surface, where this complementary surface of the protein channel can be displayed without superfluous surfaces.
The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior surfaces of protein structures. HOLLOW is written in PYTHON and is available at http://hollow.sourceforge.net.
The surface of a protein can be used to rationalize complex biochemical mechanisms. For instance, in studies of protein channels, the geometric properties of the channel openings dictate the type of substrates that can pass through the channel. Vestibules in the middle of channels can serve as staging areas of the substrate transport. Programs that identify trajectories in a protein channel (HOLE , CAVER , and MOLE ) can generate representations of the channel surface, but these surfaces are rendered at a coarse level of detail. In order to fully realize an analysis of the channel, an atomic-level visualization of the channel surface is required.
Unfortunately, in standard molecular viewers, extraneous pieces of surfaces are a persistent problem in the selective representation of molecular surfaces. The reason is that partial surfaces are, by convention, encoded as a property of an atom. Certain atoms in a protein structure may contribute to more than one surface where for example, an atom lining a channel may also form part of a void. If the surface of this atom is selected to be displayed, then both the channel and void surfaces will be displayed, where the partial surface of the void is an artifact if the area of interest is the channel.
Another common problem is the selection of channel residues. As the exterior part of the molecular surface obscures the channel surface, the exterior surface must also be removed. Typically, the viewing plane is clipped and the surface representation is restricted to the display of channel-lining residues. Unfortunately, there is no simple way to select channel residues and the channel residues must be selected manually, which is a tedious and error-prone process for the user.
To overcome these problems, we present HOLLOW, a program that produces output that can be used to generate clean visualizations of channel surfaces in a standard molecular viewer, such as PyMOL . The output of HOLLOW is a PDB file of dummy atoms that makes a "casting" of the empty volumes of a structure where the molecular surface of the dummy atoms can be shown to closely approximate the channel surface. The channel residues can also be selected by proximity to the dummy atoms. The display of this complementary surface of the dummy atoms results in a clean visualization of the channel without any unwanted additional surfaces.
HOLLOW uses dummy atoms to fill the empty space inside a structure. In the automated mode, overlapping dummy atoms are defined on a rectangular grid surrounding the molecular structure. By default, the probe radius of the dummy atoms is set to 1.4 Å and the grid-spacing to 0.5 Å. The dummy atoms are eliminated from the grid if they overlap with the molecular structure, or they are found outside the exterior envelope of the protein. To reduce the number of dummy atoms while not affecting the overall volume, dummy atoms from the interior of the block are selectively removed if this does not affect the overall volume of the block. These dummy atoms are then written to a PDB file as oxygen atoms by default, or any other atom type as specified in the configuration file. These dummy atoms constitute a global map of voids, pockets and tunnels of a protein structure.
In order to identify pockets and tunnels, an exterior envelope needs to be defined. As channels open from multiple positions of the protein, the exterior envelope is used to demarcate the end of the channel. Dummy atoms found above the envelope are eliminated. The dummy atoms below the envelope and above the protein surface correspond to the volume of pockets. In HOLLOW, the exterior envelope is defined by rolling a large 8.0 Å sphere over the surface atoms. Surface atoms are defined by the solvent-accessible surface area (SASA) by SASA > 9 Å2. Both the SASA and exterior envelope elimination are calculated using the Shrake-Rupley dot-density method .
HOLLOW allows for a wide range of customization options. All parameters, including grid spacing, probe sizes and fill atom type, are editable. In particular, there is a manual mode where the user can specify a constrained region (spherical or cylindrical) in which to calculate the dummy atoms. This allows finer grid spacing to be used with reasonable processor time.
By running HOLLOW on Rh50, dummy atoms (defined on a 0.5 Å grid) are generated to fill the channel volume. The channel residues are easily selected by proximity to the dummy atoms. The display of the molecular surface can be restricted to the surface of the channel residues, which produces a highly detailed visualization of the channel surface in atomic detail (Figure 1B). Nevertheless, there are unnecessary additional surfaces in this display (Figure 1B – left side and lower right of black solid box, lower right of dotted box, and grey box), which arise from the display of other surfaces associated with the atoms in the channel residues. In comparison, the molecular surface of the HOLLOW-generated dummy atoms is shown (Figure 1C), which clearly shows the channel lumen in atomic detail without gratuitous surfaces. Comparison to the molecular surface of the channel (atoms selected by proximity to the HOLLOW-generated dummy atoms – Figure 1B) reveals a very similar surface with only minor differences.
Compared to other surface generation programs, HOLLOW focuses on customization of surface rendering. VOIDOO  and SURFNET  generate polygon surfaces, which cannot be easily edited in molecular viewers. Instead, HOLLOW generates dummy atoms, which not only provides a convenient tool for selecting residues that line cavities by proximity to the dummy atoms, but also permits control over the rendering of partial surfaces leading to significantly clearer visualizations of channel surfaces. Indeed, the origin of HOLLOW arose from the difficulty that the authors found in generating detailed channel surfaces using standard existing programs.
HOLLOW takes a "casting" of the cavities by filling the voids, channels and pockets of a protein with dummy atoms defined on a grid. At small grid-spacing, the surface of the casting is shown to match the molecular surface of the protein. Manipulation of the dummy atoms provides a convenient way to customize the visualization of the interior surface. The size of the grid and search region can dramatically affect the calculation time, but high quality surfaces can be determined in reasonable durations on average desktop computers.
Availability and requirements
This research was supported by the Center for Membrane Protein Structure (GM73210), the Membrane Protein Expression Center (GM74929) and the Howard Hughes Medical Institute. Thanks to Ian M. Harwood and Franklin A. Hays for insightful suggestions and thanks to David A. Agard and Robert M. Stroud for support.
- Smart OS, Neduvelil JG, Wang X, Wallace BA, Sansom MSP: HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J Mol Graph Model 1996, 14(6):354. 10.1016/S0263-7855(97)00009-XView Article
- Petrek M, Otyepka M, Banas P, Kosinova P, Koca J, Damborsky J: CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 2006, 7: 316. 10.1186/1471-2105-7-316View Article
- Petrek M, Kosinova P, Koca J, Otyepka M: MOLE: A Voronoi diagram-based explorer of molecular channels, pores, and tunnels. Structure 2007, 15(11):1357–1363. 10.1016/j.str.2007.10.007View Article
- DeLano WL: The PyMOL Molecular Graphics System. Palo Alto, Ca, USA.: DeLano Scientific; 2002.
- Shrake A, Rupley JA: Environment and Exposure to Solvent of Protein Atoms – Lysozyme and Insulin. J Mol Biol 1973, 79(2):351–371. 10.1016/0022-2836(73)90011-9View Article
- Gruswitz F, Ho CM, del Rosario M, Westhoff CM, Stroud RM: Transport Mechanism of the Nitrosomonas europaea Rhesus Channel Rh50. 2008, in press.
- Kleywegt GJ, Jones TA: Detection, Delineation, Measurement and Display of Cavities in Macromolecular Structures. Acta Crystallogr D 1994, 50: 178–185. 10.1107/S0907444993011333View Article
- Laskowski RA: SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995, 13(5):323–330. 10.1016/0263-7855(95)00073-9View Article
- Connolly ML: Analytical Molecular-Surface Calculation. J Appl Crystallogr 1983, 16(Oct):548–558. 10.1107/S0021889883010985View Article
- Perutz MF, Mathews FS: An X-Ray Study of Azide Methaemoglobin. J Mol Biol 1966, 21(1):199. 10.1016/0022-2836(66)90088-XView Article
- Lerner MG, Carlson HA: APBS plugin for PyMOL. Ann Arbor: University of Michigan; 2008.
- Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA: Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci USA 2001, 98(18):10037–10041. 10.1073/pnas.181342398View Article
- Rigo A: Psyco.2007. [http://psyco.sourceforge.net/]
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