The effect of N-acetylation and N-methylation of lysine residue of Tat peptide on its interaction with HIV-1 TAR RNA

PLoS One. 2013 Oct 17;8(10):e77595. doi: 10.1371/journal.pone.0077595. eCollection 2013.

Abstract

Post-translational modification (PTM) of RNA binding proteins (RBPs) play a very important role in determining their binding to cognate RNAs and therefore regulate the downstream effects. Lysine can undergo various PTMs and thereby contribute to the regulation of different cellular processes. It can be reversibly acetylated and methylated using a pool of respective enzymes, to act as a switch for controlling the binding efficiency of RBPs. Here we have delineated the thermodynamic and kinetic effects of N-acetylation and N-monomethylation of lysine on interaction between HIV-1 TAR RNA and its cognate binder Tat peptide ( a model system). Our results indicate that acetylation of lysine 50 (K50), leads to eight- fold reduction in binding affinity, originating exclusively from entropy changes whereas, lysine 51 (K51) acetylation resulted only in three fold decrease with large enthalpy-entropy compensation. The measurement of kinetic parameters indicated major change (4.5 fold) in dissociation rate in case of K50 acetylation however, K51 acetylation showed similar effect on both association and dissociation rates. In contrast, lysine methylation did not affect the binding affinity of Tat peptide to TAR RNA at K50, nonetheless three fold enhancement in binding affinity was observed at K51 position. In spite of large enthalpy-entropy compensation, lysine methylation seems to have more pronounced position specific effect on the kinetic parameters. In case of K50 methylation, simultaneous increase was observed in the rate of association and dissociation leaving binding affinity unaffected. The increased binding affinity for methylated Tat at K51 stems from faster association rate with slightly slower dissociation rate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Amino Acid Sequence
  • Base Sequence
  • Circular Dichroism
  • HIV Long Terminal Repeat*
  • HIV-1* / chemistry
  • HIV-1* / genetics
  • HIV-1* / metabolism
  • Humans
  • Kinetics
  • Lysine / chemistry*
  • Lysine / metabolism
  • Methylation
  • Peptides / chemistry*
  • Peptides / metabolism
  • Protein Binding
  • RNA, Viral* / chemistry
  • RNA, Viral* / genetics
  • RNA, Viral* / metabolism
  • Thermodynamics
  • tat Gene Products, Human Immunodeficiency Virus / chemistry*
  • tat Gene Products, Human Immunodeficiency Virus / metabolism

Substances

  • Peptides
  • RNA, Viral
  • tat Gene Products, Human Immunodeficiency Virus
  • Lysine

Grant support

This project was financially supported by Council of Scientific and Industrial Research (CSIR), Government of India, (BSC0123 project)."The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."