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Protein Science, Vol 6, Issue 9 1849-1857, Copyright © 1997 by Cold Spring Harbor Laboratory Press

ARTICLE

Backbone makes a significant contribution to the electrostatics of {alpha}/{beta}-barrel proteins

S. RAYCHAUDHURI, F. YOUNAS, P. A. KARPLUS, C. H. FAERMAN and D. R. RIPOLL
Department of Biophysics, State University of New York at Buffalo, Buffalo, New York 14214

The electrostatic properties of seven {alpha}/{beta}-barrel enzymes selected from different evolutionary families were studied: triose phosphate isomerase, fructose-1,6-bisphosphate aldolase, pyruvate kinase, mandelate racemase, trimethylamine dehydrogenase, glycolate oxidase, and narbonin, a protein without any known enzymatic activity. The backbone of the {alpha}/{beta}-barrel has a distinct electrostatic field pattern, which is dipolar along the barrel axis. When the side chains are included in the calculations the general effect is to modulate the electrostatic pattern so that the electrostatic field is generally enhanced and is focused into a specific area near the active site. We use the electrostatic flux through a square surface near the active site to gauge the functionally relevant magnitude of the electrostatic field. The calculations reveal that in six out of the seven cases the backbone itself contributes greater than 45% of the total flux. The substantial electrostatic contribution of the backbone correlates with the known preference of {alpha}/{beta}-barrel enzymes for negatively charged substrates.
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