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

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Biological Membranes

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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.

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Authors
  1. Xiche Hu
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  2. Dong Xu
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  3. Kenneth Hamer
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  4. Klaus Schulten
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  5. Juergen Koepke
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  6. Hartmut Michel
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Editors and Affiliations

  1. Department of Chemistry, Pennsylvania State University, 152 Davey Laboratory, 16802, University Park, PA, USA

    Kenneth M. Merz Jr.

  2. Groupe de Recherche en Transport Membranaire (GRTM) Départements de physique et de chimie, Université de Montréal, C.P. 6128, succ. Centre-Ville, Montréal, Québec, Canada, H3C 3J7

    Benoît Roux

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Hu, X., Xu, D., Hamer, K., Schulten, K., Koepke, J., Michel, H. (1996). Prediction of the Structure of an Integral Membrane Protein: The Light-Harvesting Complex II of Rhodospirillum molischianum . In: Merz, K.M., Roux, B. (eds) Biological Membranes. Birkhäuser Boston. https://doi.org/10.1007/978-1-4684-8580-6_15

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  • DOI: https://doi.org/10.1007/978-1-4684-8580-6_15

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