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  Knowledge Based Structure Prediction of the Light-Harvesting Complex II of Rhodospirillum molischianum

Hu, X., Xu, D., Hamer, K., Schulten, K., Koepke, J., & Michel, H. (1996). Knowledge Based Structure Prediction of the Light-Harvesting Complex II of Rhodospirillum molischianum. In P. M. Pardalos, & D. Shalloway (Eds.), DIMACS Series in Discrete Mathematics and Theoretical Computer Science (pp. 97-122). American Mathematical Society, Providence, R.I.,.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0007-44D4-D Version Permalink: https://hdl.handle.net/21.11116/0000-000B-A22C-D
Genre: Book Chapter

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 Creators:
Hu, Xiche1, Author
Xu, Dong1, Author
Hamer, Kenneth1, Author
Schulten, Klaus1, Author
Koepke, Jürgen2, Author           
Michel, Hartmut2, Author                 
Affiliations:
1Theoretical Biophysics, Beckman Institute, University of Illinois at Urbana|Champaign, Urbana, IL 61801, USA, ou_persistent22              
2Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Max Planck Society, ou_2068290              

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Free keywords: light-harvesting complex; purple bacteria; protein folding; proteinstructure; sequence analysis
 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 αand 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 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.

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Language(s): eng - English
 Dates: 1995-111996
 Publication Status: Issued
 Pages: 26
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1090/dimacs/023/07
 Degree: -

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Title: DIMACS Series in Discrete Mathematics and Theoretical Computer Science
  Subtitle : Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding
Source Genre: Multi-Volume
 Creator(s):
Pardalos, Panayote M.1, Editor
Shalloway, David2, Editor
Xue, Guoliang3, Author
Affiliations:
1 University of Florida, Gainesville, FL, USA, ou_persistent22            
2 Cornell University, Ithaca, NY, USA, ou_persistent22            
3 University of Vermont, Burlington, VT, USA, ou_persistent22            
Publ. Info: American Mathematical Society, Providence, R.I.,
Pages: - Volume / Issue: 23 Sequence Number: - Start / End Page: 97 - 122 Identifier: DOI: 10.1090/dimacs/023
ISBN: 978-0-8218-0471-1