Side-chain effects on peptidyl-prolyl cis/trans isomerisation

Area of Science:

• Biochemistry
• Structural Biology
• Protein Folding

Background:

• Peptidyl-prolyl cis/trans isomerization is a known rate-limiting step in protein folding.
• Understanding factors controlling prolyl bond conformation is crucial for predicting protein structure and function.

Purpose of the Study:

• To investigate if the amino acid preceding proline affects the cis prolyl bond probability in native proteins.
• To systematically study the thermodynamics and kinetics of prolyl isomerization in a defined pentapeptide series.

Main Methods:

• Synthesized pentapeptide series Ac-Ala-Xaa-Pro-Ala-Lys-NH2 with all proteinogenic amino acids at the Xaa position.
• Utilized 1H-NMR and Circular Dichroism (CD) spectroscopy to analyze peptide structure.
• Employed solvent jump and 1H-NMR magnetization transfer experiments to determine isomerization kinetics and cis/trans ratios.

Main Results:

• Oligopeptides were devoid of ordered structure, isolating side-chain effects of the Xaa residue.
• A correlation was observed between cis content in oligopeptides and Xaa-Pro cis bond propensity in proteins.
• Rate constants for isomerization varied significantly, with tyrosine and histidine specifically reducing rates via side-chain deprotonation.

Conclusions:

• Local amino acid identity preceding proline is a primary determinant of prolyl bond conformation in proteins.
• These findings support the hypothesis that local effects govern prolyl bond isomerization, impacting protein folding pathways.
• Specific amino acid side chains, like tyrosine and histidine, can modulate isomerization rates through chemical modifications.