A coupled ionization-conformational equilibrium is required to understand the properties of ionizable residues in the hydrophobic interior of staphylococcal nuclease

Jinfeng Liu, Jason Swails, John Zhang, Xiao He, Adrian E. Roitberg

Research output: Contribution to journalArticle

Abstract

Ionizable residues in the interior of proteins play essential roles, especially in biological energy transduction, but are relatively rare and seem incompatible with the complex and polar environment. We perform a comprehensive study of the internal ionizable residues on 21 variants of staphylococcal nuclease with internal Lys, Glu, or Asp residues. Using pH replica exchange molecular dynamics simulations, we find that, in most cases, the pKa values of these internal ionizable residues are shifted significantly from their values in solution. Our calculated results are in excellent agreement with the experimental observations of the Garcia-Moreno group. We show that the interpretation of the experimental pKa values requires the study of not only protonation changes but also conformational changes. The coupling between the protonation and conformational equilibria suggests a mechanism for efficient pH-sensing and regulation in proteins. This study provides new physical insights into how internal ionizable residues behave in the hydrophobic interior of proteins.

Original languageEnglish (US)
Pages (from-to)1639-1648
Number of pages10
JournalJournal of the American Chemical Society
Volume140
Issue number5
DOIs
StatePublished - Feb 7 2018

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Micrococcal Nuclease
Ionization
Protonation
Proteins
Molecular Dynamics Simulation
Viperidae
Molecular dynamics
Computer simulation

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

A coupled ionization-conformational equilibrium is required to understand the properties of ionizable residues in the hydrophobic interior of staphylococcal nuclease. / Liu, Jinfeng; Swails, Jason; Zhang, John; He, Xiao; Roitberg, Adrian E.

In: Journal of the American Chemical Society, Vol. 140, No. 5, 07.02.2018, p. 1639-1648.

Research output: Contribution to journalArticle

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