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Membrane Protein Properties Revealed through Data-Rich Electrostatics Calculations
Frank V Marcoline1, Neville Bethel2, Christopher J Guerriero3
1Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
Structure (London, England : 1993)
|June 30, 2015
Summary
The enhanced APBSmem software improves calculations of membrane protein electrostatics. It identifies charged residues with high energy penalties within the membrane, aiding in understanding protein function.
Area of Science:
- Biophysics
- Computational Biology
- Structural Biology
Background:
- Electrostatic properties are crucial for understanding membrane protein biophysics, including ion channel selectivity and membrane-spanning segment stability.
- The Poisson-Boltzmann (PB) equation is a standard method for calculating protein electrostatics, with APBSmem software addressing PB equation solutions in membrane environments.
Purpose of the Study:
- To introduce significant advancements in the APBSmem software for enhanced membrane protein electrostatics calculations.
- To provide tools for automated system setup, energy decomposition, pKa shift calculation, and non-polar energy computation.
Main Methods:
- Implemented full automation of system setup and per-residue energy decomposition.
- Integrated PDB2PQR, calculated membrane-induced pKa shifts, and non-polar energies.
- Developed command-line scripting for large-scale calculations and applied to TRPV1 and 1,614 membrane proteins.
Main Results:
- Demonstrated enhanced capabilities of APBSmem on membrane proteins, including the TRPV1 ion channel.
- Conducted a large-scale survey of 1,614 membrane proteins to identify residues with significant electrostatic penalties.
- Generated a comprehensive list of residues likely to experience functional constraints due to their membrane environment.
Conclusions:
- The advanced APBSmem software offers a powerful, automated platform for detailed electrostatic analysis of membrane proteins.
- The identification of residues with high electrostatic penalties provides valuable insights into membrane protein stability and function.
- This work facilitates further research into the structure-function relationships of membrane proteins.
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