Backbone makes a significant contribution to the electrostatics of alpha/beta-barrel proteins.
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.
Raychaudhuri
S
S
Department of Biophysics, State University of New York at Buffalo 14214, USA.
Younas
F
F
Karplus
P A
PA
Faerman
C H
CH
Ripoll
D R
DR
D000429:Alcohol Oxidoreductases / Q000737:chemistry; D004798:Enzymes / Q000737:chemistry*; D005634:Fructose-Bisphosphate Aldolase / Q000737:chemistry; D005916:Globulins / Q000737:chemistry; D008958:Models, Molecular; D010089:Oxidoreductases, N-Demethylating / Q000737:chemistry; D014674:Plant Proteins, Dietary / Q000737:chemistry; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011770:Pyruvate Kinase / Q000737:chemistry; D019998:Racemases and Epimerases / Q000737:chemistry; D055672:Static Electricity; D014305:Triose-Phosphate Isomerase / Q000737:chemistry
D004798:Enzymes; D005916:Globulins; D014674:Plant Proteins, Dietary; C066193:narbonin; D000429:Alcohol Oxidoreductases; C020821:glycollate oxidase; D010089:Oxidoreductases, N-Demethylating; C023186:trimethylamine dehydrogenase; D011770:Pyruvate Kinase; D005634:Fructose-Bisphosphate Aldolase; D019998:Racemases and Epimerases; C021540:mandelate racemase; D014305:Triose-Phosphate Isomerase