Prediction of the Structure of an Integral Membrane Protein: The Light-Harvesting Complex II of Rhodospirillum molischianum

Abstract

We illustrate in this chapter how one proceeds to predict the structure of integral membrane proteins when a highly homologous structure is unknown. 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, which were independently verified by multiple sequence alignment propensity analyses and homology modeling. A consensus assignment for secondary structure was derived from a combination of all the prediction methods used. Transmembrane helices were built by comparative modeling. The resulting tertiary structures were then aggregated into a quaternary structure through molecular dynamics simulations and energy minimization under constraints provided by site directed mutagenesis and FT Resonance Raman spectra, as well as conservation of residues. The structure of LH-II, so determined, was an octamer of αβ heterodimers forming a ring with a diameter of 70 Å. We discuss how the resulting structure may be used to solve the phase problem in X-ray crystallography in a procedure called molecular replacement. We will also discuss the exciton structure which results from the circular arrangement of chlorophyls in LH-II.KeywordsIntegral Membrane ProteinTransmembrane HelixTransmembrane SegmentMolecular ReplacementResonance Raman SpectrumThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.