Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins.
BACKGROUND
Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure-function relationship. However, experimental measurement of TFEs of TMBs is challenging. Although a recent computational method can be used to calculate TFEs, the results of which are in excellent agreement with experimentally measured values, this method does not scale up, and is limited to small TMBs.


RESULTS
We have developed an approximation method that calculates TFEs of TM residues in TMBs accurately, with which depth-dependent transfer free energy profiles can be derived. Our results are in excellent agreement with experimental measurements. This method is efficient and applicable to all bacterial TMBs regardless of the size of the protein.


METHODS
An online webserver is available at http://tanto.bioe.uic.edu/tmb-tfe .


BACKGROUND
: jliang@uic.edu.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
Wei
W
Tian
Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
Meishan
M
Lin
Toyota Technological Institute at Chicago, Chicago, IL, USA.
Hammad
H
Naveed
Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
Jie
J
Liang
D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D006090:Gram-Negative Bacteria / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D001426:Bacterial Proteins; D008565:Membrane Proteins