PROTEIN-STRUCTURE MODELING OF THE BACTERIAL LIGHT-HARVESTING COMPLEX

Protein structure modelling offers a method of obtaining 3-dimensional information that can be tested and used to plan mutagenesis experimen ts when a crystallographically determined structure is not available. At its simplest a model may consist of little more than a secondary st ructure prediction coupled with a determination of the likely regions of transmembrane/membrane surface/globular configuration. These method s can yield an interesting topology map of the protein, which places t he residues in their likely positions with respect to, for example, th e membrane interface. If it is a member of a large family of related p roteins then aligned protein sequences can be used to predict the resi dues that have an important function as these will be largely conserve d in the alignments. Using all these methods a model can be constructe d (using for example, the Nicholson Molecular Modelling Kit) to visual ize the proposed structure in three dimensions following the premise o f good design, that is, avoiding obvious steric clashes, packing of he lices in a realistic manner, observing the correct II-bond lengths, et c. In this latter exercise the review of Chothia (Annu. Rev. Biochem. 53, 537-572, 1984) of the principles of protein structure is particula rly helpful as it clearly sets out how proteins pack and their preferr ed configuration. There is a wealth of information about individual am ino acid conformational preferences and observed frequencies of occurr ence in known protein structures, which can help decide how the residu es in the model can be oriented. In this article we have collated the various protein models of the bacterial light-harvesting complexes and present our own model, which is a synthesis of the available biophysi cal data and theoretical predictions, and show its performance in expl aining recent results of site-directed mutants of the LH1 and LH2 ligh t-harvesting complexes of Rhodobacter sphaeroides.