Knowledge based structure prediction of the light-harvesting complex II of rhodospirillum molischianum

Abstract

Abstract. We illustrate in this article how one proceeds to predict the structure of integral membrane proteins using a combined approach in which molecular dynamics simulations and energy minimization are performed based on structural information from conventional structure prediction methods and experimental constraints derived from biochemical and spectroscopical data. We focus here on the prediction of the structure of the light-harvesting complex II (LH-II) of Rhodospirillum molischianum, an integral membrane protein of 16 polypeptides aggregating and binding to 24 bacteriochlorophyll a's and 12 lycopenes. Hydropathy analysis was performed to identify the putative transmembrane segments. Multiple sequence alignment propensity analyses further pinpointed 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 secondary structure was derived from a combination of all the prediction methods used. The three-dimensional structures for the α-and the β-apoprotein were built by comparative modeling. The resulting tertiary structures were combined into an αβ dimer pair with bacteriochlorophyll a's attached under constraints provided by site directed mutagenesis and FT Resonance Raman spectra, as well as by conservation of residues. The αβ dimer pairs were then aggregated into a quaternary structure through molecular dynamics simulations and energy minimization. The structure of LH-II, so determined, was an octamer of αβ heterodimers forming a ring with a diameter of 70Å. We discuss how the resulting structure may be used to solve the phase problem in X-ray crystallography in a procedure called molecular replacement.

Model for the Light-Harvesting Complex I (B875) of Rhodobacter sphaeroides

“…2, was derived by means of multiple secondary structure prediction methods (Engelman et al, 1986;Persson and Argos, 1994;Geourjon and Deleage, 1994;Holley and Karplus, 1991) as had been done in the case of LH-II of Rs. molischianum (Koepke et al, 1996;Hu et al, 1995Hu et al, , 1996. Also listed in Fig.…”