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A hydrogen bonded chain in bacteriorhodopsin by computer modelling approach.
R Sankara-Ramakrishnan1, S Vishveshwara
1Molecular Bio-Physics Unit, Indian Institute of Science, Bangalore.
Journal of Biomolecular Structure & Dynamics
|August 1, 1989
Summary
Computer modeling reveals a continuous hydrogen-bonded chain (HBC) within Bacteriorhodopsin (BR) membrane-spanning helices. Two structures, including proline-induced turns, successfully model this essential chain and retinal placement.
Area of Science:
- Structural Biology
- Biophysics
- Computational Modeling
Background:
- Bacteriorhodopsin (BR) is a membrane protein crucial for proton transport.
- Its seven alpha-helical segments are key to its function.
- Understanding the internal hydrogen-bonded network is vital for elucidating BR's mechanism.
Purpose of the Study:
- To investigate the existence and conformation of a continuous Hydrogen Bonded Chain (HBC) within Bacteriorhodopsin's membrane-spanning alpha-helices.
- To model the spatial arrangement of these helices using computer simulations.
- To determine if a continuous HBC can be formed and how it relates to experimental findings, including retinal placement.
Main Methods:
- Utilized computer modeling to simulate the seven alpha-helical segments of Bacteriorhodopsin (BR).
- Employed Eulerian angles (alpha, beta, gamma) and dihedral angles (phi p-1, psi p-1) to define inter-helical orientations, especially for helices containing proline.
- Varied parameters to match experimental distances from electron diffraction studies and analyzed inter-atomic distances for hydrogen bonds.
Main Results:
- Two structural models (Structure I and Structure II) were found to support a continuous HBC.
- Structure II incorporated left-handed turns preceding proline residues in helices B, C, and F, improving the fit.
- The modeled HBC spans approximately 25Å and accommodates key residues, including Lys-216 in dual conformations, and allows for retinal placement consistent with experimental predictions.
Conclusions:
- A continuous Hydrogen Bonded Chain (HBC) is feasible within Bacteriorhodopsin's membrane-spanning helices, supporting two distinct structural models.
- The inclusion of specific conformational changes, such as left-handed turns around proline, is important for accurate modeling.
- The computational models provide insights into the structural basis of BR function, including proton pathways and chromophore interactions.