Helix formation in model peptides based on nucleolin TPAKK motifs

Area of Science:

• Biochemistry
• Molecular Biology
• Structural Biology

Background:

• Nucleolin is a key nucleolar protein involved in various cellular processes.
• The N-terminal domain of nucleolin contains a putative nucleic acid binding motif, TPAKK.
• Understanding the structural basis of nucleolin's function is crucial for deciphering its role in gene regulation and cell cycle control.

Purpose of the Study:

• To investigate the secondary structures adopted by peptide models of nucleolin's N-terminal TPAKK motif.
• To explore the influence of pH, acetylation, and solvent conditions on the peptide structures.
• To elucidate the potential mechanisms of nucleic acid interaction mediated by these structural motifs.

Main Methods:

• Circular Dichroism (CD) spectroscopy to assess secondary structure.
• Nuclear Magnetic Resonance (NMR) spectroscopy, including Nuclear Overhauser Effect (NOE) and chemical shift analysis.
• Synthesis of peptide models (TP1 and TP2) representing the TPAKK motif.

Main Results:

• CD and NMR data indicate that peptides adopt distinct structures influenced by pH and acetylation of lysine residues.
• Trifluoroethanol (TFE) induces significant structural changes, favoring helical conformations.
• NMR analysis in 0.5M NaClO4 reveals structures similar to acetylated peptides, suggesting ion interactions with lysine side chains.
• Helical structures in TPAKK motifs appear stabilized by N-capping interactions involving threonine.

Conclusions:

• The Thr-Pro sequence within TPAKK motifs can initiate short helical segments.
• These helical structures, stabilized by N-capping, are proposed to interact with nucleic acids.
• Lysine and threonine residues within these helical segments likely play a role in nucleic acid binding for nucleolin.