Abstract
The protein dipole moment is a low-resolution parameter that characterizes the second-order charge organization of a biomolecule. Theoretical approaches to calculate protein dipole moments rely on pK a values, which are either computed individually for each ionizable residue or obtained from model compounds. The influence of pK a shifts are evaluated first by comparing calculated and measured dipole moments of β-lactoglobulin. Second, calculations are made on a dataset of 66 proteins from the Protein Data Bank, and average differences are determined between dipole moments calculated with model pK as, pK as derived using a Poisson–Boltzmann approach, and empirically-calculated pK as. Dipole moment predictions that neglect pK a shifts are consistently larger than predictions in which they are included. The importance of pK a shifts are observed to vary with protein size, internal permittivity, and solution pH.
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Abbreviations
- β-Lg:
-
β-Lactoglobulin
- \( \Updelta {\text{p}}K_{\text{a}}^{\text{calc}} \) :
-
Calculated pK a shift
- \( \mu_{{}} \) :
-
Dipole moment
- \( \mu_{\text{m}} \) :
-
Dipole moment calculated using \( {\text{p}}K_{\text{a}}^{\text{m}} {\text{s}} \)
- \( \mu_{\text{pb}} \) :
-
Dipole moment calculated using \( {\text{p}}K_{\text{a}}^{\text{pb}} {\text{s}} \)
- B :
-
Estimation bias
- D :
-
Average percentage difference
- DNA:
-
Deoxyribonucleic acid
- NMR:
-
Nuclear magnetic resonance
- PDB:
-
Protein data bank
- pI:
-
Isoelectric point
- \( {\text{p}}K_{\text{a}}^{\text{calc}} \) :
-
Calculated pK a
- \( {\text{p}}K_{\text{a}}^{\text{e}} \) :
-
Empirically-calculated pK a
- \( {\text{p}}K_{\text{a}}^{\text{m}} \) :
-
Model pK a
- \( {\text{p}}K_{\text{a}}^{\text{pb}} \) :
-
Poisson–Boltzmann calculated pK a
- RNase A:
-
Ribonuclease A
- Z :
-
Formal charge of the ion
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Mellor, B.L., Khadka, S., Busath, D.D. et al. Influence of pK a Shifts on the Calculated Dipole Moments of Proteins. Protein J 30, 490–498 (2011). https://doi.org/10.1007/s10930-011-9355-8
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DOI: https://doi.org/10.1007/s10930-011-9355-8