Computing the structure of large complexes: applying constraint satisfaction techniques to modeling the 16s ribosomal rna

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abstract: Large macromolecular complexes such as the 16S ribosomal RNA (16S rRNA)frustrate traditional experimental methods of structure determination thatsucceed with smaller molecules. These large complexes often contain bothprotein and nucleic acid components composed of thousands of atoms, makingthem intractable to X-ray crystallographic techniques. Extensive biochemicalstudies of these macromolecules, however, often yield useful, though sparse,structural information by revealing particular interactions between parts ofthe macromolecular complex. This type of experimental data can beconceptualized as constraints on the three-dimensional structure of themacromolecule. Computational techniques can be used to reduce the number ofvalid molecular conformations based on satisfaction of these constraints. In this paper, we apply constraint satisfaction methodologies to produce a setof three-dimensional structures for the 16S rRNA that is consistent withexperimental data and provides an estimate of the range of valid 16S rRNAconformations. Starting with the fixed positions of the protein subunits (asdetermined by neutron diffraction experiments) as well as the predictedsecondary structure for the RNA, we determine the location of the RNA segmentsusing information about the proximity these segments to particular proteins(as determined by labelling-protection experiments). In our computations, weuse an object representation of the 16S rRNA in which helices are representedas cylindrical objects and proteins as spherical objects. Distanceconstraints between objects represent experimentally determined helix-helixand helix-protein interactions. An initially large list of possible locationsand orientations for each object is reduced by an iterative process involvingsatisfaction of these constraints. This method eventually produces a list ofvalid locations/orientations for each object. Based on these final locationlists, we can produce candidate three-dimensional structures, or coherentinstances, each of which satisfies all the constraints. The system uses anexhaustive grid search, checks distances in a direction-sensitive manner,accommodates disjunctive constraints, and checks for volume overlapviolations.

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