PREDICTING THE STRUCTURE OF THE LIGHT-HARVESTING COMPLEX-II OF RHODOSPIRILLUM-MOLISCHIANUM

We attempted to predict through computer modeling the structure of the light-harvesting complex II (LH-II) of Rhodospirillum molischianum, b efore the impending publication of the structure of a homologous prote in solved by means of X-ray diffraction. The protein studied is an int egral membrane protein of 16 independent polypeptides, 8 alpha-apoprot eins and 8 beta-apoproteins, which aggregate and bind to 24 bacterioch lorophyll-a's and 12 lycopenes. Available diffraction data of a crysta l of the protein, which could not be phased due to a lack of heavy met al derivatives, served to test the predicted structure, guiding the se arch. In order to determine the secondary structure, hydropathy analys is was performed to identify the putative transmembrane segments and m ultiple sequence alignment propensity analyses were used to pinpoint t he exact sites of the 20-residue-long transmembrane segment and the 4- residue-long terminal sequence at both ends, which were independently verified and improved by homology modeling. A consensus assignment for the secondary structure was derived from a combination of all the pre diction methods used. Three-dimensional structures for the alpha- and the beta-apoprotein were built by comparative modeling. The resulting tertiary structures are combined, using X-PLOR, into an alpha beta dim er pair with bacteriochlorophyll-a's attached under constraints provid ed by site-directed mutagenesis and spectral data. The alpha beta dime r pairs were then aggregated into a quaternary structure through furth er molecular dynamics simulations and energy minimization. The structu re of LH-II so determined is an octamer of alpha beta heterodimers for ming a ring with a diameter of 70 Angstrom.