TCB Publications - Abstract

Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Jürgen Koepke, and Hartmut Michel. Predicting the structure of the light-harvesting complex II of Rhodospirillum molischianum. Protein Science, 4:1670-1682, 1995.

HU95 We attempted to predict through computer modeling the structure of the light-harvesting complex II (LH-II) of Rhodospirillum molischianum, before the impending publication of the structure of a homologous protein solved by means of X-ray diffraction. The protein studied is an integral membrane protein of sixteen independent polypeptides, eight $\alpha$-apoproteins and eight $\beta$-apoproteins, which aggregate and bind to 24 bacteriochlorophyll a's and twelve lycopenes. Available diffraction data of a crystal of the protein, which could not be phased due to a lack of heavy metal derivatives, served to test the predicted structure, guiding the search. In order to determine the secondary structure, hydropathy analysis was performed to identify the putative transmembrane segments and multiple sequence alignment propensity analyses were used to pinpoint the exact sites of the 20 residue long transmembrane segment and the four 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 prediction 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 $\alpha\beta$ dimer pair with bacteriochlorophyll a's attached under constraints provided by site directed mutagenesis and spectral data. The $\alpha\beta$ dimer pairs were then aggregated into a quaternary structure through further molecular dynamics simulations and energy minimization. The structure of LH-II so determined is an octamer of $\alpha\beta$ heterodimers forming a ring with a diameter of 70 A.

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