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This article is part of the supplement: Highlights from the 2nd IEEE Symposium on Biological Data Visualization

Open Access Research

Exploring cavity dynamics in biomolecular systems

Norbert Lindow1*, Daniel Baum1, Ana-Nicoleta Bondar2 and Hans-Christian Hege1

Author Affiliations

1 Department of Visualization and Data Analysis, Zuse Institute Berlin, Takustr. 7, 14195 Berlin-Dahlem, Germany

2 Theoretical Molecular Biophysics, Department of Physics, Freie Universit├Ąt Berlin, Arnimallee 14, 14195 Berlin-Dahlem, Germany

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BMC Bioinformatics 2013, 14(Suppl 19):S5  doi:10.1186/1471-2105-14-S19-S5

Published: 12 November 2013

Abstract

Background

The internal cavities of proteins are dynamic structures and their dynamics may be associated with conformational changes which are required for the functioning of the protein. In order to study the dynamics of these internal protein cavities, appropriate tools are required that allow rapid identification of the cavities as well as assessment of their time-dependent structures.

Results

In this paper, we present such a tool and give results that illustrate the applicability for the analysis of molecular dynamics trajectories. Our algorithm consists of a pre-processing step where the structure of the cavity is computed from the Voronoi diagram of the van der Waals spheres based on coordinate sets from the molecular dynamics trajectory. The pre-processing step is followed by an interactive stage, where the user can compute, select and visualize the dynamic cavities. Importantly, the tool we discuss here allows the user to analyze the time-dependent changes of the components of the cavity structure. An overview of the cavity dynamics is derived by rendering the dynamic cavities in a single image that gives the cavity surface colored according to its time-dependent dynamics.

Conclusion

The Voronoi-based approach used here enables the user to perform accurate computations of the geometry of the internal cavities in biomolecules. For the first time, it is possible to compute dynamic molecular paths that have a user-defined minimum constriction size. To illustrate the usefulness of the tool for understanding protein dynamics, we probe the dynamic structure of internal cavities in the bacteriorhodopsin proton pump.