High pKa variability of cysteine residues in structural databases and the effect of H-bond contributions

MARINO S. M., Soylu I.

TURKISH JOURNAL OF BIOCHEMISTRY-TURK BIYOKIMYA DERGISI, vol.39, no.4, pp.435-739, 2014 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 39 Issue: 4
  • Publication Date: 2014
  • Doi Number: 10.5505/tjb.2014.55823
  • Journal Name: TURKISH JOURNAL OF BIOCHEMISTRY-TURK BIYOKIMYA DERGISI
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, TR DİZİN (ULAKBİM)
  • Page Numbers: pp.435-739
  • Keywords: Cysteine, redox biology, bioinformatics, biochemistry, PK(A) VALUES, PREDICTION, RATIONALIZATION, SPECIFICITY, MOLECULES
  • Akdeniz University Affiliated: Yes

Abstract

Objective: Our first objective was to extensively compare two most common empirical protein pKa predictors, propka1.0 (ppka1) and propka3.0 (ppka3); we have specifically compared them as tools for high-throughput analyses of structural datasets with a particular focus on the amino acid Cysteine (Cys); afterwards, our goal was to assess their performances with known instances of reactive Cys residues.