Predicting the structure of the light‐harvesting complex II of rhodospirillum molischianum

Xiche Hu, Dong Xu, Kenneth Hamer, Klaus Schulten, Juergen Koepke, Hartmut Michel

Research output: Contribution to journalArticlepeer-review

Abstract

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 16 independent polypeptides, 8 α-apoproteins and 8 β- apoproteins, which aggregate and bind to 24 bacteriochlorophyll-a's and 12 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 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 prediction methods used. Three-dimensional structures for the α- and the β-apoprotein were built by comparative modeling. The resulting tertiary structures are combined, using X-PLOR, into an αβ dimer pair with bacteriochlorophyll-a's attached under constraints provided by site-directed mutagenesis and spectral data. The αβ 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 αβ heterodimers forming a ring with a diameter of 70 Å.

Original languageEnglish (US)
Pages (from-to)1670-1682
Number of pages13
JournalProtein Science
Volume4
Issue number9
DOIs
StatePublished - Sep 1995

Keywords

  • integral membrane protein
  • light-harvesting complex
  • molecular replacement
  • protein folding
  • protein structure
  • purple bacteria
  • sequence analysis

ASJC Scopus subject areas

  • Biochemistry

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